Lag0017661 (gene) Sponge gourd (AG‐4) v1

Overview
NameLag0017661
Typegene
OrganismLuffa acutangula (Sponge gourd (AG‐4) v1)
DescriptionPolynucleotide phosphorylase 1
Locationchr5: 6466875 .. 6467650 (+)
RNA-Seq ExpressionLag0017661
SyntenyLag0017661
Sequences
The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide
Hold the cursor over a type above to highlight its positions in the sequence below.
ATGTGGGATCCTCAACATGCTCCAGTGCTGCCGCGGCTCAGCCGTCTCTCCTTCTTTCTCTCGCTCCAGCGCCGCCGCGAGACTCAGCCGTCTCTCTCTCTTTCTCTCGCTCTAGCGTTGCCGCAAACTCAACCGTGTCTCTCTCTTTCTCTCGCTTGTCTCTCTCTTTCTCTCGCTCCAGCGCCGCCACAAACTCAACCATTCTCTCTTTCTCGCTCCAGCTCCGATTGGATCGAGGTACGCGCTTAAGTAGGGCAACTCGAGACGTTTCACTGCATTTCCAGCCTGATTTAATGATCGGTTATATTTTCAATGGACAGCGGAAATGTTCAATTCTTCTCCTCCTCCTCCTTTGAAAAGGCTTTCACAGTATGCCCCATGTTGATTCGTGTCATGAAGGTCTGTTGATGCCCATTCCAATGTTGCAACTTGGTCTAATACTGATACAATAATTTGAAATTTACTTCACTCGTTTTCTGATTCTTTGATAGGTCCAACCTGAAAAAATTTAATCTAATCATTGGTAGTGGTGGAAAAAAGGTGAAGAGAATTATAGAAGAAACAGGAGTCGAGGCTATTGACACTCAAGATGAAGGGATAGTATGTTTACAGGAATTTCATTTAGCCAACTTAGCCAACTATGACTCTTTTGACTGCAATTTTGATATGTTTTTCTTTTGTAGGTTAAAATTACTGCAAAGGATTTCTCAAGCTTGGAAAAATCTAAAGCTATTATTAGCAATCTAACTATGGTTCCTACCGTTGGTGATATATAA

mRNA sequence

ATGTGGGATCCTCAACATGCTCCAGTGCTGCCGCGGCTCAGCCGTCTCTCCTTCTTTCTCTCGCTCCAGCGCCGCCGCGAGACTCAGCCGTCTCTCTCTCTTTCTCTCGCTCTAGCGTTGCCGCAAACTCAACCGTCGGAAATGTTCAATTCTTCTCCTCCTCCTCCTTTGAAAAGGCTTTCACAGTCCAACCTGAAAAAATTTAATCTAATCATTGGTAGTGGTGGAAAAAAGGTGAAGAGAATTATAGAAGAAACAGGAGTCGAGGCTATTGACACTCAAGATGAAGGGATAGTTAAAATTACTGCAAAGGATTTCTCAAGCTTGGAAAAATCTAAAGCTATTATTAGCAATCTAACTATGGTTCCTACCGTTGGTGATATATAA

Coding sequence (CDS)

ATGTGGGATCCTCAACATGCTCCAGTGCTGCCGCGGCTCAGCCGTCTCTCCTTCTTTCTCTCGCTCCAGCGCCGCCGCGAGACTCAGCCGTCTCTCTCTCTTTCTCTCGCTCTAGCGTTGCCGCAAACTCAACCGTCGGAAATGTTCAATTCTTCTCCTCCTCCTCCTTTGAAAAGGCTTTCACAGTCCAACCTGAAAAAATTTAATCTAATCATTGGTAGTGGTGGAAAAAAGGTGAAGAGAATTATAGAAGAAACAGGAGTCGAGGCTATTGACACTCAAGATGAAGGGATAGTTAAAATTACTGCAAAGGATTTCTCAAGCTTGGAAAAATCTAAAGCTATTATTAGCAATCTAACTATGGTTCCTACCGTTGGTGATATATAA

Protein sequence

MWDPQHAPVLPRLSRLSFFLSLQRRRETQPSLSLSLALALPQTQPSEMFNSSPPPPLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEGIVKITAKDFSSLEKSKAIISNLTMVPTVGDI
Homology
BLAST of Lag0017661 vs. NCBI nr
Match: XP_022147753.1 (probable polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X2 [Momordica charantia])

HSP 1 Score: 121.3 bits (303), Expect = 6.0e-24
Identity = 68/91 (74.73%), Postives = 73/91 (80.22%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM NSSPPP        PL  + +   +K NLIIGSGGKKVK IIEETGVEAIDTQD+G
Sbjct: 668 AEMLNSSPPPSKRLSQYAPLIHVMKVQPEKINLIIGSGGKKVKSIIEETGVEAIDTQDDG 727

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           IVKITAKD SSLEKSKAIISNLTMVPTVGDI
Sbjct: 728 IVKITAKDLSSLEKSKAIISNLTMVPTVGDI 758

BLAST of Lag0017661 vs. NCBI nr
Match: XP_022147752.1 (probable polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X1 [Momordica charantia])

HSP 1 Score: 121.3 bits (303), Expect = 6.0e-24
Identity = 68/91 (74.73%), Postives = 73/91 (80.22%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM NSSPPP        PL  + +   +K NLIIGSGGKKVK IIEETGVEAIDTQD+G
Sbjct: 668 AEMLNSSPPPSKRLSQYAPLIHVMKVQPEKINLIIGSGGKKVKSIIEETGVEAIDTQDDG 727

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           IVKITAKD SSLEKSKAIISNLTMVPTVGDI
Sbjct: 728 IVKITAKDLSSLEKSKAIISNLTMVPTVGDI 758

BLAST of Lag0017661 vs. NCBI nr
Match: KAF3442818.1 (hypothetical protein FNV43_RR16736 [Rhamnella rubrinervis])

HSP 1 Score: 118.6 bits (296), Expect = 3.9e-23
Identity = 67/91 (73.63%), Postives = 72/91 (79.12%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           SEM  SSPPP        PL  + + N +K NLIIGSGGKKVK IIEETGVEAIDTQD+G
Sbjct: 710 SEMSKSSPPPSRRLSNYAPLIHVMKVNPEKVNLIIGSGGKKVKSIIEETGVEAIDTQDDG 769

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           IVKITAKD SSLEK+K IISNLTMVPTVGDI
Sbjct: 770 IVKITAKDLSSLEKAKTIISNLTMVPTVGDI 800

BLAST of Lag0017661 vs. NCBI nr
Match: KAF3441239.1 (hypothetical protein FNV43_RR15152 [Rhamnella rubrinervis])

HSP 1 Score: 118.6 bits (296), Expect = 3.9e-23
Identity = 66/91 (72.53%), Postives = 73/91 (80.22%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM  SSPPP        PL  + + N +K NLIIGSGGKKVK IIEETGVEA+DTQD+G
Sbjct: 642 AEMSKSSPPPSRRLSNYAPLIHVMKVNPEKVNLIIGSGGKKVKSIIEETGVEAVDTQDDG 701

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           IVKITAKD SSLEK+KAIISNLTMVPTVGDI
Sbjct: 702 IVKITAKDLSSLEKAKAIISNLTMVPTVGDI 732

BLAST of Lag0017661 vs. NCBI nr
Match: PON42102.1 (Polyribonucleotide nucleotidyltransferase [Trema orientale])

HSP 1 Score: 117.1 bits (292), Expect = 1.1e-22
Identity = 65/91 (71.43%), Postives = 72/91 (79.12%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM  SSPPP        PL  + +   +K NLIIG+GGKKVK IIEETGVEAIDTQD+G
Sbjct: 705 AEMLKSSPPPSRKLSKYAPLIHVMKVKPEKINLIIGTGGKKVKSIIEETGVEAIDTQDDG 764

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           IVKITAKD SSLEKSKA+ISNLTMVPTVGDI
Sbjct: 765 IVKITAKDLSSLEKSKALISNLTMVPTVGDI 795

BLAST of Lag0017661 vs. ExPASy Swiss-Prot
Match: Q69LE7 (Probable polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Oryza sativa subsp. japonica OX=39947 GN=PNP1 PE=2 SV=1)

HSP 1 Score: 100.9 bits (250), Expect = 1.1e-20
Identity = 57/91 (62.64%), Postives = 66/91 (72.53%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM   SPPP        PL  + +    K NLIIGSGGK +K IIEETGV+AIDT D+G
Sbjct: 675 NEMSKCSPPPAKVLSPYAPLIHVMKVKPNKVNLIIGSGGKTIKSIIEETGVDAIDTGDDG 734

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
            VKITA+D SSLEKSKAII+NLTMVP VG+I
Sbjct: 735 TVKITARDLSSLEKSKAIIANLTMVPKVGEI 765

BLAST of Lag0017661 vs. ExPASy Swiss-Prot
Match: Q8GZQ3 (Polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=PNP1 PE=1 SV=1)

HSP 1 Score: 90.5 bits (223), Expect = 1.5e-17
Identity = 53/91 (58.24%), Postives = 64/91 (70.33%), Query Frame = 0

Query: 46  SEMFNSSPPP--------PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEG 105
           +EM   SPPP        PL  + + +  K   +IGSGGKKVK IIEE+GVEAID QD+G
Sbjct: 674 AEMAKCSPPPTLSLSKYAPLILIMKVHPSKVYSLIGSGGKKVKSIIEESGVEAIDMQDDG 733

Query: 106 IVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
            VKI A D +SLE++KAIIS LTMVP+VGDI
Sbjct: 734 TVKIMAIDVASLERAKAIISGLTMVPSVGDI 764

BLAST of Lag0017661 vs. ExPASy Swiss-Prot
Match: Q6MDI2 (Polyribonucleotide nucleotidyltransferase OS=Protochlamydia amoebophila (strain UWE25) OX=264201 GN=pnp PE=3 SV=2)

HSP 1 Score: 56.6 bits (135), Expect = 2.4e-07
Identity = 40/97 (41.24%), Postives = 56/97 (57.73%), Query Frame = 0

Query: 34  LSLALALPQTQPSEMFNSSPPPPLKRLSQSNLK--KFNLIIGSGGKKVKRIIEETGVEAI 93
           L+  LA+  T   EM   +P     R+    +K  K  ++IG GGK+++ IIE+TGV+ I
Sbjct: 535 LNKMLAVCPTYKGEMSRYAP-----RIETIQIKPSKIAVVIGPGGKQIRAIIEQTGVQ-I 594

Query: 94  DTQDEGIVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           D  D G+V I A D  S+EK+KAII  LT    +G I
Sbjct: 595 DIDDTGLVNIAAIDLVSIEKAKAIIHGLTAEIEIGRI 625

BLAST of Lag0017661 vs. ExPASy Swiss-Prot
Match: C0R0E0 (Polyribonucleotide nucleotidyltransferase OS=Brachyspira hyodysenteriae (strain ATCC 49526 / WA1) OX=565034 GN=pnp PE=3 SV=1)

HSP 1 Score: 53.1 bits (126), Expect = 2.6e-06
Identity = 28/73 (38.36%), Postives = 45/73 (61.64%), Query Frame = 0

Query: 56  PLKRLSQSNLKKFNLIIGSGGKKVKRIIEETGVEAIDTQDEGIVKITAKDFSSLEKSKAI 115
           P  +    N +K  ++IG GGK +K IIEETG + ++ QD G+V I A D  +L+K+  +
Sbjct: 550 PKYKTMDVNPEKIRVLIGPGGKNIKAIIEETGSD-VEIQDSGVVNIFAPDTPTLDKTIKL 609

Query: 116 ISNLTMVPTVGDI 129
           I++    P VG++
Sbjct: 610 INSYVKDPEVGEV 621

BLAST of Lag0017661 vs. ExPASy Swiss-Prot
Match: B8CW78 (Polyribonucleotide nucleotidyltransferase OS=Halothermothrix orenii (strain H 168 / OCM 544 / DSM 9562) OX=373903 GN=pnp PE=3 SV=1)

HSP 1 Score: 52.4 bits (124), Expect = 4.5e-06
Identity = 41/108 (37.96%), Postives = 59/108 (54.63%), Query Frame = 0

Query: 21  SLQRRRETQPSLSLSLALALPQTQPSEMFNSSPPPPLKRLSQSNLKKFNLIIGSGGKKVK 80
           +L+R RE +  +   +   + + +P      SP  PL    + +  K   IIG GGK + 
Sbjct: 528 ALKRAREGRLYILDKMLQVIDKPRP----ELSPYAPLMITMKVSPDKIRHIIGPGGKIIN 587

Query: 81  RIIEETGVEAIDTQDEGIVKITAKDFSSLEKSKAIISNLTMVPTVGDI 129
           +II+ETGVE ID  D+G V I A+D  S  ++K II+ LT    VGDI
Sbjct: 588 KIIDETGVE-IDIDDDGSVYILAQDQESGNRAKEIINKLTKEVEVGDI 630

The following BLAST results are available for this feature:
Match NameE-valueIdentityDescription
XP_022147753.16.0e-2474.73probable polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X2 [... [more]
XP_022147752.16.0e-2474.73probable polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X1 [... [more]
KAF3442818.13.9e-2373.63hypothetical protein FNV43_RR16736 [Rhamnella rubrinervis][more]
KAF3441239.13.9e-2372.53hypothetical protein FNV43_RR15152 [Rhamnella rubrinervis][more]
PON42102.11.1e-2271.43Polyribonucleotide nucleotidyltransferase [Trema orientale][more]
Match NameE-valueIdentityDescription
Q69LE71.1e-2062.64Probable polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Oryza sat... [more]
Q8GZQ31.5e-1758.24Polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Arabidopsis thalia... [more]
Q6MDI22.4e-0741.24Polyribonucleotide nucleotidyltransferase OS=Protochlamydia amoebophila (strain ... [more]
C0R0E02.6e-0638.36Polyribonucleotide nucleotidyltransferase OS=Brachyspira hyodysenteriae (strain ... [more]
B8CW784.5e-0637.96Polyribonucleotide nucleotidyltransferase OS=Halothermothrix orenii (strain H 16... [more]
InterPro
Analysis Name: InterPro Annotations of Sponge gourd (AG-4) v1
Date Performed: 2022-08-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR004088K Homology domain, type 1PFAMPF00013KH_1coord: 68..117
e-value: 9.9E-6
score: 25.3
IPR036612K Homology domain, type 1 superfamilyGENE3D3.30.1370.10K Homology domain, type 1coord: 53..127
e-value: 4.0E-12
score: 47.8
IPR036612K Homology domain, type 1 superfamilySUPERFAMILY54791Eukaryotic type KH-domain (KH-domain type I)coord: 66..120
NoneNo IPR availablePANTHERPTHR11252:SF12POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, CHLOROPLASTICcoord: 47..128
NoneNo IPR availablePROSITEPS50084KH_TYPE_1coord: 71..116
score: 10.734828
IPR012162Polyribonucleotide nucleotidyltransferasePANTHERPTHR11252POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASEcoord: 47..128

Relationships

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

Feature NameUnique NameType
Lag0017661.1Lag0017661.1mRNA


GO Annotation
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0000958 mitochondrial mRNA catabolic process
biological_process GO:0000965 mitochondrial RNA 3'-end processing
biological_process GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic
biological_process GO:0006402 mRNA catabolic process
cellular_component GO:0005829 cytosol
cellular_component GO:0005739 mitochondrion
molecular_function GO:0000175 3'-5'-exoribonuclease activity
molecular_function GO:0004654 polyribonucleotide nucleotidyltransferase activity
molecular_function GO:0003723 RNA binding