Spg016189 (gene) Sponge gourd (cylindrica) v1

Overview


Name	Spg016189
Type	gene
Organism	Luffa cylindrica (Sponge gourd (cylindrica) v1)
Description	Nuclear nucleic acid-binding protein C1D
Location	scaffold9: 44040154 .. 44042492 (-)
RNA-Seq Expression	Spg016189
Synteny	Spg016189

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: five_prime_UTRpolypeptideCDSthree_prime_UTR

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

TCTCAAGACACTGAGATCGGAAGCGTGTCCGGCCAAACTGCCGCCATAAACCTCTTCCAGTTCGAACCCAAAAGCCCTACCCGTGCCTTTTCCCCTCTGCAAATTAACAACGACGACGGTCCAAGCTCCCCTTCGCCGTCGCCGTCGCCATCGCAAATCATCTCCTTCTAAGGATTTGAATTTCACATCTTGGGTTTCTGTGTGAGCCCGTGAAATAGACGGAGTTCAAAATTTGGGGCAAATATGGAGGGAGGTGTTCGAGAATCCGCTGTGGTGCCCGAGAAAGTGATGGATTCAGTGAAGAAGACATTGGACAATGTAGAACAAGTCCAAACTCACCTTATTTCCTTCCTGTCTATCGCCGAGCCTGATGTTCTTGCTCAAATGCAGCCTCTCCAACGGGCTCAGTCTATGCTTTTGCTTGCTAGAGCCACTACCACTCTCTTCGCATGTAAATTTTTTTGATTACTTGTCATTATACTGGATTTGTTTCTCTTGTTTTTTGGATTATGGAGGCGAAATTTTTGTTTGTTTTGGTGAATTTTAGTAAAGTTGAGGTGTAGCGGAGTTCACCCTGATGATCATCCTATCAAGTCAGAGCTTGTAATTATTCTCATACCTTGTATCTGGTGATTAAAACTGAAATTTTCTCATATGGGTAGTAATGTTATTCTCCCATTGCTTTTGAAAAGAATCATTCTTATTCTTTCTTATGCATGTAGGAGAGATTAAGCTTGTATCAAGACAAACTAGAACGGTTCATAGGCTTGAGTAAAGGTATGTTTGAGTTTTGATTTTTAGTTTATATCAGCATCGTCTGTTTCTTTATTGTTGCTGCTTCCTTTCACAGTAGATTGATGATTTTGCATTTAAATTTGTTCATGAAGCACCATTGAAGCGATCTACTACCTTGAACTATCAAGCTGCTACTCGCTTTATTGAACATTCTCTGCCTGATCTCACCCAAGGTTGGTTAATTTGTTTGCTTTTTTGTTCTGGGGAGGGGGGTTGTGTGCTTGATTCCCTTTGATCAAGGAAATATTCCGATATTTTCAGATCAAAAGCAGAGTATGAGGGATATTAGTAGGGGAAAGGGACCAAGTGTGAAGCAACTAGAGAGGAATGTACAAAAGAAGAGGAAGTATCAGTCTTCAGAAAAACAATCTGTTCAAATTGCTGCTAAGGAGTTTCTTGAGAAAGCAGCGCGTGAGCTTCTTGGTGACAGTAATGGAGGTTTGCAGGGACCATTATGTGGGGACGCTTCAGATGATGATGACCTGCAGGAGGATTGAATTCCGGATTTCACTTGGTACCTGTTTATCACATTTATTTCTAATTTGGGCGTCCTTCTCTTTCAATAAATGCTAGTTTTTCCATATGATTGATGCTAGAATAAGATTTGATTTTCTTAATAAATTTTCCATTTTAGTTCTATTGCTCATTCTTGTGCTACTGCTTGTTGTTAGCTTGCTTAGCTTAGCGTATGGATTGCGAGTTTTAAATACAGAATGTAGTCTGTTTCTGGACCTCTTTGATGTGTTTTTACATTGTGATATGTATATCATGTTATGTTATCATTGTCAAGCCAAGGCCTTTATGCATTATTGCAGCAAAGTTTCAACTGCAATGATATAGTTTTTCTTCAATTGGAACTGTTTCCCTTCCCTCACCAAACTGAGGGCCAAGTAAACTTGAATGGTTTTTTTGTTTACTCCATGTAAATATAACACTTCCCTTCATAGAAATATGTGCGTGTGCGCGTGTATTCAATTATGTTTTGATTCTTTCTCACTTTACATCTTTCAGGAATATGAAAACCAGATTCACCTGTGCCCTTAATAACCCAACTCCTGAAGAATTGGTCCATTTTGAAGTTGGAGAGGATCGTCGGTTTTCTTTTTCTTTCCTTCTCCTAGTTTTTCCCTACAACATTAAGTCGTTTTCCCTTTACTTTATTTAAAAGTCTTCATATATATGCATTGGGAGTTTCAGTTCCATCATAAGTTTCTATTAGGACAGGACCTGGTTGGGATTTTGGCATTCTACTCTTTCTCACAGGCCGATCTTCCTGTTTGCTTCCTCCCCAATTTTTTAGAACTAGTGTGATCATATGAACAAGACATGATCTTGATAAAAGGAGTCCGTGCTTTTTACATGTAAAGTAGCCTACTTTGGTAGCTGACTTTCTAGTTCTTTTGGGGTCTGTATATCAGTCATCATCTTGTCATGTGGATTAGTCTTTTGCCATAAATTAATAATAGTATGTTCTTTGTGATAAACCACCTCCAAGAATCTTGTTTTGTTTTTCATATGGGCTCTGTTAAGTTTCTTGTTTTAAT

mRNA sequence

ATGGAGGGAGGTGTTCGAGAATCCGCTGTGGTGCCCGAGAAAGTGATGGATTCAGTGAAGAAGACATTGGACAATGTAGAACAAGTCCAAACTCACCTTATTTCCTTCCTGTCTATCGCCGAGCCTGATGTTCTTGCTCAAATGCAGCCTCTCCAACGGGCTCAGTCTATGCTTTTGCTTGCTAGAGCCACTACCACTCTCTTCGCATTAAAGTTGAGGTGTAGCGGAGTTCACCCTGATGATCATCCTATCAAGTCAGAGCTTGTAATTATTCTCATACCTTGTATCTGGTGA

Coding sequence (CDS)

ATGGAGGGAGGTGTTCGAGAATCCGCTGTGGTGCCCGAGAAAGTGATGGATTCAGTGAAGAAGACATTGGACAATGTAGAACAAGTCCAAACTCACCTTATTTCCTTCCTGTCTATCGCCGAGCCTGATGTTCTTGCTCAAATGCAGCCTCTCCAACGGGCTCAGTCTATGCTTTTGCTTGCTAGAGCCACTACCACTCTCTTCGCATTAAAGTTGAGGTGTAGCGGAGTTCACCCTGATGATCATCCTATCAAGTCAGAGCTTGTAATTATTCTCATACCTTGTATCTGGTGA

Protein sequence

MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLLARATTTLFALKLRCSGVHPDDHPIKSELVIILIPCIW

Homology

[Close]

BLAST of Spg016189 vs. NCBI nr
Match: XP_022939979.1 (nuclear nucleic acid-binding protein C1D-like [Cucurbita moschata] >XP_022939980.1 nuclear nucleic acid-binding protein C1D-like [Cucurbita moschata])

HSP 1 Score: 166.0 bits (419), Expect = 1.6e-37
Identity = 85/88 (96.59%), Postives = 87/88 (98.86%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEKVMDSVK TLDNVEQVQTHLISFLSIAEPDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKVMDSVKMTLDNVEQVQTHLISFLSIAEPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. NCBI nr
Match: XP_023524382.1 (nuclear nucleic acid-binding protein C1D-like [Cucurbita pepo subsp. pepo])

HSP 1 Score: 164.5 bits (415), Expect = 4.7e-37
Identity = 84/88 (95.45%), Postives = 87/88 (98.86%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEKVMDSVK TLDNVEQV+THLISFLSIAEPDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKVMDSVKMTLDNVEQVKTHLISFLSIAEPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. NCBI nr
Match: KAG6608310.1 (Nuclear nucleic acid-binding protein C1D, partial [Cucurbita argyrosperma subsp. sororia])

HSP 1 Score: 164.5 bits (415), Expect = 4.7e-37
Identity = 84/89 (94.38%), Postives = 87/89 (97.75%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEKVMDSVK TLDNVEQVQTHLISFLSIA PDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKVMDSVKMTLDNVEQVQTHLISFLSIAGPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSELV 90
          +RATTTLFALKLRCSGVHPDDHPIKSEL+
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSELI 89

[Close]

BLAST of Spg016189 vs. NCBI nr
Match: KAG7037658.1 (Nuclear nucleic acid-binding protein C1D [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 163.3 bits (412), Expect = 1.0e-36
Identity = 84/88 (95.45%), Postives = 86/88 (97.73%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEKVMDSVK TLDNVEQVQTHLISFLSIA PDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKVMDSVKMTLDNVEQVQTHLISFLSIAGPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. NCBI nr
Match: XP_022981849.1 (nuclear nucleic acid-binding protein C1D-like [Cucurbita maxima] >XP_022981850.1 nuclear nucleic acid-binding protein C1D-like [Cucurbita maxima])

HSP 1 Score: 162.5 bits (410), Expect = 1.8e-36
Identity = 83/88 (94.32%), Postives = 86/88 (97.73%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEK MDSVK TLD+VEQVQTHLISFLSIAEPDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKAMDSVKMTLDSVEQVQTHLISFLSIAEPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. ExPASy Swiss-Prot
Match: Q5XJ97 (Nuclear nucleic acid-binding protein C1D OS=Danio rerio OX=7955 GN=c1d PE=2 SV=1)

HSP 1 Score: 49.3 bits (116), Expect = 2.9e-05
Identity = 25/77 (32.47%), Postives = 46/77 (59.74%), Query Frame = 0


Query: 12 PEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLLARATTTLFALK 71
          P ++ D++     ++  VQ  + + +S++  D L ++ PL++A+  L+ A A  ++F + 
Sbjct: 11 PTEIEDNLNDFDSSLSSVQNMVQTLVSVSRSDRLLKLDPLEQAKLDLMSAYALNSMFWMY 70

Query: 72 LRCSGVHPDDHPIKSEL 89
          L   GV+P DHPIK EL
Sbjct: 71 LVTQGVNPKDHPIKQEL 87

[Close]

BLAST of Spg016189 vs. ExPASy TrEMBL
Match: A0A6J1FIR0 (Nuclear nucleic acid-binding protein C1D OS=Cucurbita moschata OX=3662 GN=LOC111445751 PE=3 SV=1)

HSP 1 Score: 166.0 bits (419), Expect = 7.8e-38
Identity = 85/88 (96.59%), Postives = 87/88 (98.86%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEKVMDSVK TLDNVEQVQTHLISFLSIAEPDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKVMDSVKMTLDNVEQVQTHLISFLSIAEPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. ExPASy TrEMBL
Match: A0A6J1J0U0 (Nuclear nucleic acid-binding protein C1D OS=Cucurbita maxima OX=3661 GN=LOC111480869 PE=3 SV=1)

HSP 1 Score: 162.5 bits (410), Expect = 8.6e-37
Identity = 83/88 (94.32%), Postives = 86/88 (97.73%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPEK MDSVK TLD+VEQVQTHLISFLSIAEPDVLAQM+PLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPEKAMDSVKMTLDSVEQVQTHLISFLSIAEPDVLAQMRPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +RATTTLFALKLRCSGVHPDDHPIKSEL
Sbjct: 61 SRATTTLFALKLRCSGVHPDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. ExPASy TrEMBL
Match: A0A0A0L118 (Nuclear nucleic acid-binding protein C1D OS=Cucumis sativus OX=3659 GN=Csa_4G651890 PE=3 SV=1)

HSP 1 Score: 159.8 bits (403), Expect = 5.6e-36
Identity = 83/88 (94.32%), Postives = 84/88 (95.45%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVR+ AVVPEKVMDSVK TLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL
Sbjct: 1  MEGGVRDFAVVPEKVMDSVKTTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          AR TTTLFALKLRCSGVH DDHPIKSEL
Sbjct: 61 ARVTTTLFALKLRCSGVHLDDHPIKSEL 88

[Close]

BLAST of Spg016189 vs. ExPASy TrEMBL
Match: A0A6J1CLD8 (Nuclear nucleic acid-binding protein C1D OS=Momordica charantia OX=3673 GN=LOC111012672 PE=3 SV=1)

HSP 1 Score: 157.5 bits (397), Expect = 2.8e-35
Identity = 78/88 (88.64%), Postives = 85/88 (96.59%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVRESAVVPE  MDSVKKTLDNVE+V+THLISFLSI+EP+VLAQMQPLQRAQSMLLL
Sbjct: 1  MEGGVRESAVVPESAMDSVKKTLDNVEEVRTHLISFLSISEPEVLAQMQPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          AR TTTLF+LK+RCSGVHPDDHP+KSEL
Sbjct: 61 ARITTTLFSLKVRCSGVHPDDHPVKSEL 88

[Close]

BLAST of Spg016189 vs. ExPASy TrEMBL
Match: A0A6J1IN17 (Nuclear nucleic acid-binding protein C1D OS=Cucurbita maxima OX=3661 GN=LOC111476708 PE=3 SV=1)

HSP 1 Score: 156.4 bits (394), Expect = 6.2e-35
Identity = 79/88 (89.77%), Postives = 84/88 (95.45%), Query Frame = 0


Query: 1  MEGGVRESAVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQSMLLL 60
          MEGGVR+SAVVPEKVMDSVK TL+NVEQVQTHLIS LSIAEP+VLAQMQPLQRAQSMLLL
Sbjct: 1  MEGGVRDSAVVPEKVMDSVKTTLENVEQVQTHLISLLSIAEPEVLAQMQPLQRAQSMLLL 60

Query: 61 ARATTTLFALKLRCSGVHPDDHPIKSEL 89
          AR TTTLFALK+RCSGVHPDDHPI +EL
Sbjct: 61 ARVTTTLFALKVRCSGVHPDDHPINTEL 88

[Close]

BLAST of Spg016189 vs. TAIR 10
Match: AT5G25080.1 (Sas10/Utp3/C1D family )

HSP 1 Score: 93.6 bits (231), Expect = 9.4e-20
Identity = 49/93 (52.69%), Postives = 68/93 (73.12%), Query Frame = 0


Query: 1  MEGGVRES-----AVVPEKVMDSVKKTLDNVEQVQTHLISFLSIAEPDVLAQMQPLQRAQ 60
          MEGG   S      VVPE  +++V +TL  +++++  L   L++AEP+VLA MQPLQRA+
Sbjct: 1  MEGGGGSSGGGAGGVVPESAIEAVNQTLAYLKELKPQLEQMLTLAEPEVLAAMQPLQRAK 60

Query: 61 SMLLLARATTTLFALKLRCSGVHPDDHPIKSEL 89
          +M LLA ATTTL+ L+LRC+GV PDDH +KSE+
Sbjct: 61 TMHLLAEATTTLYELRLRCTGVDPDDHRVKSEI 93

The following BLAST results are available for this feature:

BLAST of Spg016189 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_022939979.1	1.6e-37	96.59	nuclear nucleic acid-binding protein C1D-like [Cucurbita moschata] >XP_022939980...	[more]
XP_023524382.1	4.7e-37	95.45	nuclear nucleic acid-binding protein C1D-like [Cucurbita pepo subsp. pepo]	[more]
KAG6608310.1	4.7e-37	94.38	Nuclear nucleic acid-binding protein C1D, partial [Cucurbita argyrosperma subsp....	[more]
KAG7037658.1	1.0e-36	95.45	Nuclear nucleic acid-binding protein C1D [Cucurbita argyrosperma subsp. argyrosp...	[more]
XP_022981849.1	1.8e-36	94.32	nuclear nucleic acid-binding protein C1D-like [Cucurbita maxima] >XP_022981850.1...	[more]

BLAST of Spg016189 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q5XJ97	2.9e-05	32.47	Nuclear nucleic acid-binding protein C1D OS=Danio rerio OX=7955 GN=c1d PE=2 SV=1	[more]

BLAST of Spg016189 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1FIR0	7.8e-38	96.59	Nuclear nucleic acid-binding protein C1D OS=Cucurbita moschata OX=3662 GN=LOC111...	[more]
A0A6J1J0U0	8.6e-37	94.32	Nuclear nucleic acid-binding protein C1D OS=Cucurbita maxima OX=3661 GN=LOC11148...	[more]
A0A0A0L118	5.6e-36	94.32	Nuclear nucleic acid-binding protein C1D OS=Cucumis sativus OX=3659 GN=Csa_4G651...	[more]
A0A6J1CLD8	2.8e-35	88.64	Nuclear nucleic acid-binding protein C1D OS=Momordica charantia OX=3673 GN=LOC11...	[more]
A0A6J1IN17	6.2e-35	89.77	Nuclear nucleic acid-binding protein C1D OS=Cucurbita maxima OX=3661 GN=LOC11147...	[more]

BLAST of Spg016189 vs. TAIR 10


Match Name	E-value	Identity	Description
AT5G25080.1	9.4e-20	52.69	Sas10/Utp3/C1D family	[more]

InterPro

Analysis Name: InterPro Annotations of Sponge gourd (cylindrica) v1
Date Performed: 2022-08-01


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR007146	Sas10/Utp3/C1D	PFAM	PF04000	Sas10_Utp3	coord: 23..89 e-value: 5.5E-7 score: 30.1
None	No IPR available	PANTHER	PTHR15341:SF5	EXOSOME-ASSOCIATED FACTOR RRP47/DNA STRAND REPAIR C1D-RELATED	coord: 11..89
IPR011082	Exosome-associated factor Rrp47/DNA strand repair C1D	PANTHER	PTHR15341	SUN-COR STEROID HORMONE RECEPTOR CO-REPRESSOR	coord: 11..89

Relationships

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


Feature Name	Unique Name	Type
Spg016189.1	Spg016189.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0000460	maturation of 5.8S rRNA
biological_process	GO:0010468	regulation of gene expression
cellular_component	GO:0005737	cytoplasm
cellular_component	GO:0000178	exosome (RNase complex)
cellular_component	GO:0005730	nucleolus
molecular_function	GO:0003677	DNA binding
molecular_function	GO:0003723	RNA binding