Cla012979 (gene) Watermelon (97103) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cla012979
Type	gene
Organism	Citrullus. lanatus (Watermelon (97103) v1)
Description	Cleavage and polyadenylation specificity factor subunit 3 (AHRD V1 **-- B0WXD2_CULQU)
Location	Chr9 : 22156826 .. 22158592 (-)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDS

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGAAAAACGTCAAACGTAGGCTTGCAAGGTATGCCAAATGTTACTTGCTCATTGAACATGTGCAAATATACTTCAAATATTTGCTATGCTTAACCAACACATATAGTAATGCTAAATTAACTCCAAGGCAACAAATCAATCAACATATTTAGCTGCAATGCGTACTGAACATGTCAATCAACCTCTTAGCTCATACAAGCCTTGATCTTCAATGAATATAAGTTTGGAAGGCCAAAATACAACATAAGAGAAATGAAATATAGAGAAAATAGAGGGGAAGTGGAGAGGAGGCTAAAGATTTCTTGGTGTTGGGGTGTTCTTTCATCTAATGTCGAAGGGTCTCTTTTATAGAGTCTCGAGAGCACTATGGCGCTAAGGATGGCTCTGTGGCACTATCCCTTTCCTTAAATTTCTTTTTTCTTTATTTGCAGCAGTGCTGCAATGCTCTTGGTAGTGCCGCAGTTCTAAGGGACAACACCGCGACGCTTCTTGAAACTTCAGCTACTGCCTTCAATGCCATGGATGGTGCTACACGGTGCTGTGGCAAAGGTGCATCCACGGTCATTTTCTCCTTCATTTGACCTAGTTTCCTCTTTTGGGCTTTACGCTTTAGTTTCAATTAAGCTTGGTTTTTGTCCAAATCTCAATTCTACCACCTTATTGCCGGAGACCTACAGAATCATCAAATAAACACATAAAGTACACAAACAAACTTGAATTAAACTGAGTCAGATAGTACATTTTAGGTGTTATCATTGGTCTTCTAGTGAAATAAAGGAGAGTTTCCTGTTGGCTGTTCCTGATGGTTTTTCATTGGTATGGCACTTTAGCATTTGTGTTCACTGCAAAAATATTTTTATTGTTAATCTTCCAATATTTGTCTTCTGCAGGTCTACATATGCAACAACCATACGTGATTCTAAATATGGCCGTGAGAGAGAATTTCTTAAAGCTGTATGTATAAATTAATTAATAAAATTATTTTCCCGGATTTGCCTTTTCTGCGCCTTCAAGGTTTTTTTAGAAATTGGATAAGTTGATTTTTCATTCATGTTATGCGTTCTGGTATAATAATAATTCAGGAGCCAGGAGGACATCATTAAGGTATATTGAAGTTGCATCATGTTCCAAGTACAACTTGGCATATTGGTGATATTAGGGATAGACTTCAGAATGATATATTTTATGTCCCTCGGTGAAGAAAAGAAAATATTCTGTTTTGTTTTAGGGTTTATTTTGTGATGGTTCAAGACTGTAGGTTGGTTGATGCCTTTTTGTGTAGGATATTGCATGTCATAGCTGTAGACTAACTAATCATAGTTGAGGACTGTGATATAATATAGAAACTGGTTACGACTTATGAGTGGCTATTGAGCATTGGTTGGTGACTTAAATCCGTCATAAACTCTTAATTGTTCAAGAGATACTGAATTATTTTAACTTTAAAATTTATAACTTATAGCAATGGAATTATTTGAAACATGATCGTTTTCCCGAATGATTTGATATAGGTTCATAATTGTGTGGCTAGTGGAGGGAAGGTCCTTATTCCTACTTTTGCACTTGGACGGGCTCAGGTACTTTACTGAATATTGGGTGTGGCTTTTAAATCTTTTACTGCCATCTGCATCTCTCATGACTAATTTGCTCTTGTTATATATAAAACTTTCCATTATGAACAGGAACTCTGTATCTTGTTGGATGACTATTGGGAGCGTATGAGTCTGAAGGTTCCGATATACTATTCAGCAGGTCCCTTTGAATAA

mRNA sequence

ATGAAAAACGTCAAACGTAGGCTTGCAAGGAGCCAGGAGGACATCATTAAGGTTCATAATTGTGTGGCTAGTGGAGGGAAGGTCCTTATTCCTACTTTTGCACTTGGACGGGCTCAGGAACTCTGTATCTTGTTGGATGACTATTGGGAGCGTATGAGTCTGAAGGTTCCGATATACTATTCAGCAGGTCCCTTTGAATAA

Coding sequence (CDS)

ATGAAAAACGTCAAACGTAGGCTTGCAAGGAGCCAGGAGGACATCATTAAGGTTCATAATTGTGTGGCTAGTGGAGGGAAGGTCCTTATTCCTACTTTTGCACTTGGACGGGCTCAGGAACTCTGTATCTTGTTGGATGACTATTGGGAGCGTATGAGTCTGAAGGTTCCGATATACTATTCAGCAGGTCCCTTTGAATAA

Protein sequence

MKNVKRRLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAGPFE

Homology

[Close]

BLAST of Cla012979 vs. Swiss-Prot
Match: CPS3B_ARATH (Cleavage and polyadenylation specificity factor subunit 3-II OS=Arabidopsis thaliana GN=CPSF73-II PE=1 SV=2)

HSP 1 Score: 88.6 bits (218), Expect = 2.8e-17
Identity = 39/54 (72.22%), Postives = 45/54 (83.33%), Query Frame = 1


Query: 10  RSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R +E +  VH CVA GGK LIP+FALGRAQELC+LLDDYWERM++KVPIY+S+G
Sbjct: 216 REREFLQAVHKCVAGGGKALIPSFALGRAQELCMLLDDYWERMNIKVPIYFSSG 269

[Close]

BLAST of Cla012979 vs. Swiss-Prot
Match: INT11_HUMAN (Integrator complex subunit 11 OS=Homo sapiens GN=CPSF3L PE=1 SV=2)

HSP 1 Score: 80.5 bits (197), Expect = 7.6e-15
Identity = 37/54 (68.52%), Postives = 42/54 (77.78%), Query Frame = 1


Query: 10  RSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R ++ + KVH  V  GGKVLIP FALGRAQELCILL+ +WERM+LKVPIY+S G
Sbjct: 217 RERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETFWERMNLKVPIYFSTG 270

[Close]

BLAST of Cla012979 vs. Swiss-Prot
Match: INT11_MOUSE (Integrator complex subunit 11 OS=Mus musculus GN=Cpsf3l PE=1 SV=1)

HSP 1 Score: 80.5 bits (197), Expect = 7.6e-15
Identity = 37/54 (68.52%), Postives = 42/54 (77.78%), Query Frame = 1


Query: 10  RSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R ++ + KVH  V  GGKVLIP FALGRAQELCILL+ +WERM+LKVPIY+S G
Sbjct: 217 RERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETFWERMNLKVPIYFSTG 270

[Close]

BLAST of Cla012979 vs. Swiss-Prot
Match: INT11_RAT (Integrator complex subunit 11 OS=Rattus norvegicus GN=Cpsf3l PE=2 SV=1)

HSP 1 Score: 80.5 bits (197), Expect = 7.6e-15
Identity = 37/54 (68.52%), Postives = 42/54 (77.78%), Query Frame = 1


Query: 10  RSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R ++ + KVH  V  GGKVLIP FALGRAQELCILL+ +WERM+LKVPIY+S G
Sbjct: 217 RERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETFWERMNLKVPIYFSTG 270

[Close]

BLAST of Cla012979 vs. Swiss-Prot
Match: INT11_PONAB (Integrator complex subunit 11 OS=Pongo abelii GN=CPSF3L PE=2 SV=2)

HSP 1 Score: 80.5 bits (197), Expect = 7.6e-15
Identity = 37/54 (68.52%), Postives = 42/54 (77.78%), Query Frame = 1


Query: 10  RSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R ++ + KVH  V  GGKVLIP FALGRAQELCILL+ +WERM+LKVPIY+S G
Sbjct: 217 RERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETFWERMNLKVPIYFSTG 270

[Close]

BLAST of Cla012979 vs. TrEMBL
Match: B9HVV0_POPTR (Metallo-beta-lactamase family protein OS=Populus trichocarpa GN=POPTR_0010s11650g PE=4 SV=2)

HSP 1 Score: 96.7 bits (239), Expect = 1.1e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 213 KYAREREFLKAVHECVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 269

[Close]

BLAST of Cla012979 vs. TrEMBL
Match: U5G1X1_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0010s11650g PE=4 SV=1)

HSP 1 Score: 96.7 bits (239), Expect = 1.1e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 52  KYAREREFLKAVHECVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 108

[Close]

BLAST of Cla012979 vs. TrEMBL
Match: M0SCM1_MUSAM (Uncharacterized protein OS=Musa acuminata subsp. malaccensis PE=4 SV=1)

HSP 1 Score: 96.7 bits (239), Expect = 1.1e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 224 KYAREREFLRAVHKCVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 280

[Close]

BLAST of Cla012979 vs. TrEMBL
Match: A0A061E8Z1_THECC (Cleavage and polyadenylation specificity factor 73 kDa subunit-II OS=Theobroma cacao GN=TCM_011055 PE=4 SV=1)

HSP 1 Score: 96.3 bits (238), Expect = 1.5e-17
Identity = 44/57 (77.19%), Postives = 51/57 (89.47%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R  R +E +  VHNCVA+GGKVLIPTFALGRAQELCILL+DYWERM+LKVPIY+S+G
Sbjct: 212 RYGREREFLKAVHNCVAAGGKVLIPTFALGRAQELCILLEDYWERMNLKVPIYFSSG 268

[Close]

BLAST of Cla012979 vs. TrEMBL
Match: A0A0A0LQW3_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_2G435430 PE=4 SV=1)

HSP 1 Score: 95.5 bits (236), Expect = 2.6e-17
Identity = 44/57 (77.19%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VHNC+ASGGKVLIPTFALGRAQELC+LLDDYWERM+LK PIY SAG
Sbjct: 213 KYAREREFLKAVHNCLASGGKVLIPTFALGRAQELCVLLDDYWERMNLKFPIYVSAG 269

[Close]

BLAST of Cla012979 vs. NCBI nr
Match: gi|823255818|ref|XP_012460570.1| (PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II [Gossypium raimondii])

HSP 1 Score: 97.4 bits (241), Expect = 9.7e-18
Identity = 45/57 (78.95%), Postives = 51/57 (89.47%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           R  R +E +  VHNCVA+GGKVLIPTFALGRAQELCILL+DYWERM+LKVPIY+SAG
Sbjct: 212 RYGREREFLKAVHNCVAAGGKVLIPTFALGRAQELCILLEDYWERMNLKVPIYFSAG 268

[Close]

BLAST of Cla012979 vs. NCBI nr
Match: gi|566190304|ref|XP_002314781.2| (metallo-beta-lactamase family protein [Populus trichocarpa])

HSP 1 Score: 96.7 bits (239), Expect = 1.6e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 213 KYAREREFLKAVHECVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 269

[Close]

BLAST of Cla012979 vs. NCBI nr
Match: gi|743822724|ref|XP_011021767.1| (PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II isoform X2 [Populus euphratica])

HSP 1 Score: 96.7 bits (239), Expect = 1.6e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 185 KYAREREFLKAVHECVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 241

[Close]

BLAST of Cla012979 vs. NCBI nr
Match: gi|695009560|ref|XP_009391419.1| (PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II [Musa acuminata subsp. malaccensis])

HSP 1 Score: 96.7 bits (239), Expect = 1.6e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CVA GGKVLIPTFALGRAQELCILLDDYWERM+LKVPIY+SAG
Sbjct: 213 KYAREREFLRAVHKCVAGGGKVLIPTFALGRAQELCILLDDYWERMNLKVPIYFSAG 269

[Close]

BLAST of Cla012979 vs. NCBI nr
Match: gi|1021027988|gb|KZM85775.1| (hypothetical protein DCAR_026803 [Daucus carota subsp. sativus])

HSP 1 Score: 96.7 bits (239), Expect = 1.6e-17
Identity = 45/57 (78.95%), Postives = 50/57 (87.72%), Query Frame = 1


Query: 7   RLARSQEDIIKVHNCVASGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYYSAG 64
           + AR +E +  VH CV +GGKVLIPTFALGRAQELCILLDDYWERMSLKVPIY+SAG
Sbjct: 213 KYAREREFLDAVHKCVTNGGKVLIPTFALGRAQELCILLDDYWERMSLKVPIYFSAG 269

The following BLAST results are available for this feature:

BLAST of Cla012979 vs. Swiss-Prot


Match Name	E-value	Identity	Description
CPS3B_ARATH	2.8e-17	72.22	Cleavage and polyadenylation specificity factor subunit 3-II OS=Arabidopsis thal...	[more]
INT11_HUMAN	7.6e-15	68.52	Integrator complex subunit 11 OS=Homo sapiens GN=CPSF3L PE=1 SV=2	[more]
INT11_MOUSE	7.6e-15	68.52	Integrator complex subunit 11 OS=Mus musculus GN=Cpsf3l PE=1 SV=1	[more]
INT11_RAT	7.6e-15	68.52	Integrator complex subunit 11 OS=Rattus norvegicus GN=Cpsf3l PE=2 SV=1	[more]
INT11_PONAB	7.6e-15	68.52	Integrator complex subunit 11 OS=Pongo abelii GN=CPSF3L PE=2 SV=2	[more]

BLAST of Cla012979 vs. TrEMBL


Match Name	E-value	Identity	Description
B9HVV0_POPTR	1.1e-17	78.95	Metallo-beta-lactamase family protein OS=Populus trichocarpa GN=POPTR_0010s11650...	[more]
U5G1X1_POPTR	1.1e-17	78.95	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0010s11650g PE=4 SV=1	[more]
M0SCM1_MUSAM	1.1e-17	78.95	Uncharacterized protein OS=Musa acuminata subsp. malaccensis PE=4 SV=1	[more]
A0A061E8Z1_THECC	1.5e-17	77.19	Cleavage and polyadenylation specificity factor 73 kDa subunit-II OS=Theobroma c...	[more]
A0A0A0LQW3_CUCSA	2.6e-17	77.19	Uncharacterized protein OS=Cucumis sativus GN=Csa_2G435430 PE=4 SV=1	[more]

BLAST of Cla012979 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|823255818\|ref\|XP_012460570.1\|	9.7e-18	78.95	PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II [Gossypi...	[more]
gi\|566190304\|ref\|XP_002314781.2\|	1.6e-17	78.95	metallo-beta-lactamase family protein [Populus trichocarpa]	[more]
gi\|743822724\|ref\|XP_011021767.1\|	1.6e-17	78.95	PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II isoform ...	[more]
gi\|695009560\|ref\|XP_009391419.1\|	1.6e-17	78.95	PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II [Musa ac...	[more]
gi\|1021027988\|gb\|KZM85775.1\|	1.6e-17	78.95	hypothetical protein DCAR_026803 [Daucus carota subsp. sativus]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR001279	Metallo-B-lactamas

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0010197	polar nucleus fusion
cellular_component	GO:0005634	nucleus
molecular_function	GO:0003674	molecular_function

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
WMU57878	watermelon EST collection version 2.0	transcribed_cluster

Relationships

The following mRNA feature(s) are a part of this gene:


Feature Name	Unique Name	Type
Cla012979	Cla012979.1	mRNA

The following transcribed_cluster feature(s) are associated with this gene:


Feature Name	Unique Name	Type
WMU57878	WMU57878	transcribed_cluster

InterPro

Analysis Name: InterPro Annotations of watermelon (97103)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR001279	Metallo-beta-lactamase	GENE3D	G3DSA:3.60.15.10		coord: 9..52 score: 5.
IPR001279	Metallo-beta-lactamase	unknown	SSF56281	Metallo-hydrolase/oxidoreductase	coord: 17..61 score: 3.16
None	No IPR available	PANTHER	PTHR11203	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR	coord: 5..63 score: 9.5
None	No IPR available	PANTHER	PTHR11203:SF37	INTEGRATOR COMPLEX SUBUNIT 11	coord: 5..63 score: 9.5

Synteny

The following gene(s) are orthologous to this gene:

None

The following gene(s) are paralogous to this gene:

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cla012979	Cucurbita pepo (Zucchini)	cpewmB274
Cla012979	Cucurbita pepo (Zucchini)	cpewmB686
Cla012979	Bottle gourd (USVL1VR-Ls)	lsiwmB044
Cla012979	Cucumber (Gy14) v2	cgybwmB100
Cla012979	Melon (DHL92) v3.6.1	medwmB086
Cla012979	Silver-seed gourd	carwmB0417
Cla012979	Silver-seed gourd	carwmB1054
Cla012979	Cucumber (Chinese Long) v3	cucwmB114
Cla012979	Watermelon (97103) v2	wmwmbB043
Cla012979	Wax gourd	wgowmB354
Cla012979	Cucumber (Gy14) v1	cgywmB580
Cla012979	Cucurbita maxima (Rimu)	cmawmB510
Cla012979	Cucurbita maxima (Rimu)	cmawmB549
Cla012979	Cucurbita moschata (Rifu)	cmowmB503
Cla012979	Cucurbita moschata (Rifu)	cmowmB541
Cla012979	Wild cucumber (PI 183967)	cpiwmB107
Cla012979	Melon (DHL92) v3.5.1	mewmB087
Cla012979	Watermelon (Charleston Gray)	wcgwmB009
Cla012979	Cucumber (Chinese Long) v2	cuwmB102