Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyribonucleotide nucleotidyltransferase 1, mitochondrial.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11784 g11784.t1 TSS g11784.t1 18397454 18397454
chr_1 g11784 g11784.t1 isoform g11784.t1 18397547 18400601
chr_1 g11784 g11784.t1 exon g11784.t1.exon1 18397547 18397600
chr_1 g11784 g11784.t1 cds g11784.t1.CDS1 18397547 18397600
chr_1 g11784 g11784.t1 exon g11784.t1.exon2 18397677 18397743
chr_1 g11784 g11784.t1 cds g11784.t1.CDS2 18397677 18397743
chr_1 g11784 g11784.t1 exon g11784.t1.exon3 18397815 18397842
chr_1 g11784 g11784.t1 cds g11784.t1.CDS3 18397815 18397842
chr_1 g11784 g11784.t1 exon g11784.t1.exon4 18398054 18398098
chr_1 g11784 g11784.t1 cds g11784.t1.CDS4 18398054 18398098
chr_1 g11784 g11784.t1 exon g11784.t1.exon5 18398155 18398363
chr_1 g11784 g11784.t1 cds g11784.t1.CDS5 18398155 18398363
chr_1 g11784 g11784.t1 exon g11784.t1.exon6 18398430 18398640
chr_1 g11784 g11784.t1 cds g11784.t1.CDS6 18398430 18398640
chr_1 g11784 g11784.t1 exon g11784.t1.exon7 18398704 18399444
chr_1 g11784 g11784.t1 cds g11784.t1.CDS7 18398704 18399444
chr_1 g11784 g11784.t1 exon g11784.t1.exon8 18399506 18399576
chr_1 g11784 g11784.t1 cds g11784.t1.CDS8 18399506 18399576
chr_1 g11784 g11784.t1 exon g11784.t1.exon9 18399667 18400601
chr_1 g11784 g11784.t1 cds g11784.t1.CDS9 18399667 18400601
chr_1 g11784 g11784.t1 TTS g11784.t1 NA NA

Sequences

>g11784.t1 Gene=g11784 Length=2361
ATGAAACCAATAGCAGCAGATGAAATGTTTCCAGAAGGAATTGATGTAGACGATCAGAGT
GCAGTAGTTCTTGATAGTCTTCATGATGGTCAGAAAGATATACATTCAGATTTCTTTAAT
GATTTCGATGATTTATTTGATGAAGAGGACAGTTCCACATCAAAATATGAAGCAAACGTT
GAGTTTAGCAATGGGCGAAAGATGACATTTAATACGGGAAATTTAGCTAAATTTACTGAT
GGATGCGTGGTTGTGAAAACAGGCGATACAGCAGTAATGTGCACAGCAATAAGTAGCAAA
AAGGCATCTAGTTCTGCTTCATTTCTTCCATTATCTGTCGATTATAGGTTAAAAAGTAGC
GCTGCCGGTCGAATACCAACAAATTACATGCGAAGAGAATTTGGGTCAACTGAAAAAGAA
ATTTTAGCATCACGTTTAGTTGATCGATCTATTAGGCCACTATTTTCAAAAGATTATCGT
TTTGAAACTCAAATAGTATGCAATGTTCTCTCTGTCGATTCTTTAAATAAACCTGATGTT
AATGCAATTAATGCTGCTTCAGCAGCCCTTCATTTAAGCGACATTCCATGGAATGGTCCT
ATAGGCGCAGTGAGAGTTGGATTATTCAAAAATGATCTGATAATAAATCCAACAAGACGA
GAACTTCAGGTATCAGACTTGGATTTGATAGTTGTTGCAACAAAACAAAATTTAGTTGTA
ATGCTTGAAGGACGAGGAAACATTGTTTTGTTACCAAACATATTGAAAGCAATTAAGCAA
GGAACTCGTGAAGCTCAATTTATAATAGATAAAATTGAAAAAATGCGAAAAGAATTGCCA
AATGTAAAACCAAAAAGAGAAGAACAAGAAATGAATATAATGGATGAAGAAATGTTGGTT
GCCTTGAAAACAATGAGTGAAATGCGCCTCAAAGATGTTTTTAGAAATACTTCTCATGAT
AAAATAAGCAGAGATCAAGCTGTACAAGTTATAAGACAAGAAGTTATAACTTCATTGCGA
TCAAGTTTTCCAGATTCTGATTTAGCAATAATTAGTGATGAATTTAACAGGCAAACAATT
TCTACATTCAGAGATTTTGTTCTTGAAGAAAACGTTCGTTGCGATGGACGAGATTTTGAT
GAATTAAGAAAAATTTCTTGTGAAGTTGATATCTTAAAAGCTTTACATGGATCTGCATTA
TTTACACGTGGACAAACTCAAGTATTATGTACAGTAACGCTTGATTCGAAAGAGAGTGCT
TTAAAATTAGATTCTTTGACTGCACTTGAGAGTGGTGTAAAAGAGAAAAATTTTTTTCTC
CATTACGAATTTCCTCCATATAGTATAGGTGAAATAGGTCGTATTGGTGCAGTGAATCGA
CGCGAAATTGGACATGGAGCACTTGCAGAAAAAGGACTTTTACCAGTATTACCTCCAAAT
TCACCTTTCACTATACGCTTAAATGCTGAAGTACTTGAGTCGAACGGTTCAAGCTCAATG
GCAACTGTTTGTGCAGGAAGTTTGGCATTACTGGATGCTGGAATACCTTTATCTTCATTA
GCATCAGGTGTCGCAATAGGATTAATATCAAAATATGAAAACAATGACACAAAACATATT
GAAAACTACAAAATTTTAACAGATCAATTAGGTATTGAAGACTACATGGGTGACATGGAT
ATGAAAGTGGCAGGAACAAAAAAAGGAATTACTTCTATACAAACAGATGTAAAAATTCCT
GGTATTCCACTTAAAATAATCAATGAGTGCCTTCAAAAAGCAACTGATGCAAAAAGTGAA
ATAATCGACATTATGAGAGAATGTATTGATGCACCTCGTTCCGAAAAGAAAGAATCATGG
CCAGTTACTGAAAAAATGACAATTGAGCCTCACATGAGATCAAAAATAATTGGTCCTGGC
GGTATTAATATCAAGCAAATGTACTTTGAGACAGGTGTTCAAATGACACAAATTGATGAA
TCTACGTTTGAAGTATTTGCACCTTCTCAATCTGCTATGGATGAAGCAAAAGAGTTTATG
CAGAAACTTATGGAAAAAGATCGCGTTCCTGATCTTGATTTTGGTGGAATATATACTGCC
AAAATTGTTGAATTGAGAGACATTGGTGTAATGGTTACTTTATACCCATCAATGCCACCT
GCTCTTCTTCATAATTCACAACTTGATATAAGAAAAGTAGCACATCCATCAGCATTAGGT
CTTGAAGTTGGACAAGAAATTACTGTAAAATATTTTGGAAGAGATCCTGTATCGGGCCTA
ATGAGATTGTCAAGAAAAGTTCTGCAGAGTCCCGCTAGTGTTAGAGTAAAAAATTTAGAC
AAAACAAGTGAGAATAGATAA

>g11784.t1 Gene=g11784 Length=786
MKPIAADEMFPEGIDVDDQSAVVLDSLHDGQKDIHSDFFNDFDDLFDEEDSSTSKYEANV
EFSNGRKMTFNTGNLAKFTDGCVVVKTGDTAVMCTAISSKKASSSASFLPLSVDYRLKSS
AAGRIPTNYMRREFGSTEKEILASRLVDRSIRPLFSKDYRFETQIVCNVLSVDSLNKPDV
NAINAASAALHLSDIPWNGPIGAVRVGLFKNDLIINPTRRELQVSDLDLIVVATKQNLVV
MLEGRGNIVLLPNILKAIKQGTREAQFIIDKIEKMRKELPNVKPKREEQEMNIMDEEMLV
ALKTMSEMRLKDVFRNTSHDKISRDQAVQVIRQEVITSLRSSFPDSDLAIISDEFNRQTI
STFRDFVLEENVRCDGRDFDELRKISCEVDILKALHGSALFTRGQTQVLCTVTLDSKESA
LKLDSLTALESGVKEKNFFLHYEFPPYSIGEIGRIGAVNRREIGHGALAEKGLLPVLPPN
SPFTIRLNAEVLESNGSSSMATVCAGSLALLDAGIPLSSLASGVAIGLISKYENNDTKHI
ENYKILTDQLGIEDYMGDMDMKVAGTKKGITSIQTDVKIPGIPLKIINECLQKATDAKSE
IIDIMRECIDAPRSEKKESWPVTEKMTIEPHMRSKIIGPGGINIKQMYFETGVQMTQIDE
STFEVFAPSQSAMDEAKEFMQKLMEKDRVPDLDFGGIYTAKIVELRDIGVMVTLYPSMPP
ALLHNSQLDIRKVAHPSALGLEVGQEITVKYFGRDPVSGLMRLSRKVLQSPASVRVKNLD
KTSENR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g11784.t1 CDD cd11364 RNase_PH_PNPase_2 381 612 1.20708E-132
20 g11784.t1 Coils Coil Coil 258 278 -
19 g11784.t1 Gene3D G3DSA:3.30.230.70 GHMP Kinase 41 280 7.0E-70
15 g11784.t1 Gene3D G3DSA:1.10.10.400 - 294 379 1.1E-24
18 g11784.t1 Gene3D G3DSA:3.30.230.70 GHMP Kinase 380 612 8.3E-77
17 g11784.t1 Gene3D G3DSA:3.30.1370.10 - 613 685 1.4E-26
16 g11784.t1 Gene3D G3DSA:2.40.50.140 - 693 769 1.5E-8
6 g11784.t1 PANTHER PTHR11252 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 57 782 3.1E-271
7 g11784.t1 PANTHER PTHR11252:SF0 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL 57 782 3.1E-271
21 g11784.t1 PIRSF PIRSF005499 PNPase 54 786 1.4E-244
1 g11784.t1 Pfam PF15004 Myeloma-overexpressed-like 1 50 4.6E-11
3 g11784.t1 Pfam PF01138 3’ exoribonuclease family, domain 1 66 196 2.5E-17
2 g11784.t1 Pfam PF03725 3’ exoribonuclease family, domain 2 199 262 9.5E-13
4 g11784.t1 Pfam PF01138 3’ exoribonuclease family, domain 1 381 516 5.4E-23
5 g11784.t1 Pfam PF00013 KH domain 623 680 1.2E-5
25 g11784.t1 ProSiteProfiles PS50084 Type-1 KH domain profile. 621 680 10.462
26 g11784.t1 ProSiteProfiles PS50126 S1 domain profile. 695 766 11.494
23 g11784.t1 SMART SM00322 kh_6 620 685 9.6E-5
10 g11784.t1 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 64 196 2.89E-39
13 g11784.t1 SUPERFAMILY SSF55666 Ribonuclease PH domain 2-like 190 279 5.89E-19
8 g11784.t1 SUPERFAMILY SSF46915 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 283 383 3.92E-18
9 g11784.t1 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 363 560 3.34E-44
14 g11784.t1 SUPERFAMILY SSF55666 Ribonuclease PH domain 2-like 510 617 1.27E-21
11 g11784.t1 SUPERFAMILY SSF54791 Eukaryotic type KH-domain (KH-domain type I) 609 698 1.21E-11
12 g11784.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 689 768 1.61E-7
24 g11784.t1 TIGRFAM TIGR03591 polynuc_phos: polyribonucleotide nucleotidyltransferase 64 766 1.2E-207

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006396 RNA processing BP
GO:0003723 RNA binding MF
GO:0004654 polyribonucleotide nucleotidyltransferase activity MF
GO:0006402 mRNA catabolic process BP
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values