Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable proline–tRNA ligase, 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_3 g3376 g3376.t1 TTS g3376.t1 24962028 24962028
chr_3 g3376 g3376.t1 isoform g3376.t1 24962131 24965665
chr_3 g3376 g3376.t1 exon g3376.t1.exon1 24962131 24962428
chr_3 g3376 g3376.t1 cds g3376.t1.CDS1 24962131 24962428
chr_3 g3376 g3376.t1 exon g3376.t1.exon2 24962494 24962620
chr_3 g3376 g3376.t1 cds g3376.t1.CDS2 24962494 24962620
chr_3 g3376 g3376.t1 exon g3376.t1.exon3 24962686 24963928
chr_3 g3376 g3376.t1 cds g3376.t1.CDS3 24962686 24963928
chr_3 g3376 g3376.t1 exon g3376.t1.exon4 24964293 24965210
chr_3 g3376 g3376.t1 cds g3376.t1.CDS4 24964293 24965210
chr_3 g3376 g3376.t1 exon g3376.t1.exon5 24965266 24965517
chr_3 g3376 g3376.t1 cds g3376.t1.CDS5 24965266 24965517
chr_3 g3376 g3376.t1 exon g3376.t1.exon6 24965570 24965665
chr_3 g3376 g3376.t1 cds g3376.t1.CDS6 24965570 24965665
chr_3 g3376 g3376.t1 TSS g3376.t1 24965667 24965667

Sequences

>g3376.t1 Gene=g3376 Length=2934
ATGAACCGCTTGTCAAAAATATTTTTTCCACAACTTATTGTGCCGAAAAATGCAATTGTC
AAAAGTCATGAAGTACAACAATCTAAAAGTCAAAAGTTAATGATAGATTGCGGTTTAATA
AAACATTGCAATAATGGAACATATTACATATTACCTTTACTACAAAGATCAATTGAGAAA
TTAACAAAAATCATTGATCATTATATGACAGAAATCGATGGTCAAAAAATTACTATGCCC
ACATTAACATCAGCAGACTTATGGAAAAAATCTGGGAGATTTGAAAATGCAGTAACTGAA
TTGATGACAGTCAATGATAGGCATAATAGACTTCAAATTCTTAGTCCTACACATGAGGAA
TCAGTGACAAACTTAATTGCATCTATTTCTCCAGTCTCTTACAAAAGCTTTCCTCTTCGT
CTTTATCAAATTACACCTAAATTTCGAGATGAGTTAAGACCAAAATTTGGATTATTGAGA
GCAAAAGAGTTTTTAATGAAGGATATGTACACCTTTGATATTGGATTAAATGAGGCTAAA
AAGACATATGATGAAGTTAATGAACAATATGTCAAAATTTTCAATCATTTGAATGTATCC
TTTATAAAAATTGGCGCTGATACTGGTAATATGGGCGGAAATATTTCTCATGAATTTCAT
ATAGCAAGTTCTATTGGCGAAGATTCAATCATTTCATGTACATCTTGTTCAAAAGCTATT
AATGTTGAATTGGCAAAAGATGGAAAAATATGTGAACAATGTAAAATTGATGATCTTAAA
CGTCAGCAAGGAATTGAAATTGGTCACACATTTATTCTTGAAGATAGGTATTCAAAAGTG
TTAAATGCTACATTTTTAAATAAAACTGGAAAACCAGAAAATATTCAAATGGGTTGTTAT
GGAATCGGTGTGACTCGTCTTATAGCAGCAGTAATTGAACTTTTCTCAAACGAAAATGAA
ATCAGATGGTCAGATGCAATAGCACCATACAAAATTTGTATTATTCCACCAAAGGAAGGA
AGCAAAGAAGAGGAGTCTGTTAAGCATTTAAGCAATGAAATTTATCATTATCTGACTACT
AATTCATCACAACTTGCGGATGATATTATTGTAGATGATCGAACACACATGACAATTGGT
AAACGGTTGAAAGAGATCAAGAAACTTGGAATACCTTATATTATAGTTATTGGATCAAAA
TCAGCTGATATAAGTTCTACAATAGAAGTTCATAATTTGAGAGAAAATGTAGCCATAGAT
ATGAGTGTTGATTCCGATTATGAGATAATTAAGCTCGATCCAAATGTTATTTATGAAACA
GATGATGATGAGGATTTATTGAAAGAAGAGGAATATGTTGAGAAACAAAGATCTGCTAAA
AATTGTGAAAATGCGGCCGAATTTGTTTTCATCGACGAAATCAACAAAACAAAAAATGAG
GAAGAAGATAATAAACAAATGGTAGATGATATCATTGATAAAAAGTCAAGTGCAGAATCA
AACGACTTGCCTAATGAGGTAATTATAGAGCAAAAACCTCGTAAAAAACTGAATTTAGCG
GAATATAAAATTGTGCGTGCTAATAGACCTGCACCAATTGTCGAAGAATGCGAAAAAGTT
GTGCTCGAATTATGTGAAAATATTCCTGAAACTCTTCCAATTATTGAATTGCCAACTGAT
CCTCGAAGCATTAAAGCTCTTCTTTCTGCTCAAAATCAGCAGCCGCAACCTCAATCAATA
TCTCAACCTGAACCAATGCAAATTGATAAAGCTTTAAATATGAAAGAAGAAGAAAAAGTT
CCAAAAGAAGTAGATCCAGATTATGAAGAAATTGTTTTAATATCAATGGAATGCAATACA
GATATATCAATTTCACCACAAGAGAATGATGAGCAATTGGAAACAAAAGCTCCAGCCAAA
TTTCTTACAAATATCGTCAATACTATTAAGAAAGACGAATACGCAAAAACTTTGCTTAGT
TCTTCAACGACTCTCTTTTCTAGTATTAATGCAGTAGTTCATGAAAAGTGTAATTCGTTG
AATGAAGCAACTATTGAAAATAGCAGTAGTCGCAAGAACTCAGAACATGGTGAGAACAAA
ATTATAATGCATTTGCGAAAAGATCGGATACGACCTAAATGCTCAAGTTTTGCTATGCAA
ACAGAAAATTCTCCACTCTTTCCACCGCTTTTATTGTCACCTGATATTATTTTCAATCGT
ATCAAAAATGTAAGAAATTTCCGAAGAAAATCACGAACTCGTAGTAGAAGCCGATCAAGA
AGTAGAAGTTTTAGTCCAGAAAATGATTATTATAAACGTAGCAATTATAAATATTCACGT
TCATTACACTCTTCTACTGTGAATAGTAGCGAATTTGATTCATCAGAAAGTGACAGTTCT
GCCTATAGCTCATGTCGTTCATCAGATTACGATTCAATTAGAAAATTCGATAATAGAATA
TCAGGGCAAAGATATCGTAATCATAGATCATCTAATTATACTTACGAAGAGGAAAGAAAA
GTCGTTTATATTGGTGGGTTAACTGAAGATGTAACAAAAGAGGATTTACGTCGAAATTTT
TTAAAATATGGAACGATAAAAAAGATTTCTATTCATGCAAAGCAAGATGTTAATGGTAAT
TTACGTTTTGGTTTCATTACATTTGCTGAAGCTTCAGCTGCCTATGATGTTCTTGATAAA
TTTAAACTAGATTCGTCATTGTGTGATTATGACATTCGTTTTGGAGGGAGAAGAAGGTTT
TGCAAACAGTCTTATGCTGATTTGGATTCTTTGCCTAAAGAAGATGACATTGATGATGTA
TATAATAACAACAATATTAATATTAACAACACGATGAAATCCAAAAAAGCTGCCGAATTA
AGTTTTGAGGAACTTTTAAATATTGCCCGTCAAAAAATGTGCAGAAATAACTAA

>g3376.t1 Gene=g3376 Length=977
MNRLSKIFFPQLIVPKNAIVKSHEVQQSKSQKLMIDCGLIKHCNNGTYYILPLLQRSIEK
LTKIIDHYMTEIDGQKITMPTLTSADLWKKSGRFENAVTELMTVNDRHNRLQILSPTHEE
SVTNLIASISPVSYKSFPLRLYQITPKFRDELRPKFGLLRAKEFLMKDMYTFDIGLNEAK
KTYDEVNEQYVKIFNHLNVSFIKIGADTGNMGGNISHEFHIASSIGEDSIISCTSCSKAI
NVELAKDGKICEQCKIDDLKRQQGIEIGHTFILEDRYSKVLNATFLNKTGKPENIQMGCY
GIGVTRLIAAVIELFSNENEIRWSDAIAPYKICIIPPKEGSKEEESVKHLSNEIYHYLTT
NSSQLADDIIVDDRTHMTIGKRLKEIKKLGIPYIIVIGSKSADISSTIEVHNLRENVAID
MSVDSDYEIIKLDPNVIYETDDDEDLLKEEEYVEKQRSAKNCENAAEFVFIDEINKTKNE
EEDNKQMVDDIIDKKSSAESNDLPNEVIIEQKPRKKLNLAEYKIVRANRPAPIVEECEKV
VLELCENIPETLPIIELPTDPRSIKALLSAQNQQPQPQSISQPEPMQIDKALNMKEEEKV
PKEVDPDYEEIVLISMECNTDISISPQENDEQLETKAPAKFLTNIVNTIKKDEYAKTLLS
SSTTLFSSINAVVHEKCNSLNEATIENSSSRKNSEHGENKIIMHLRKDRIRPKCSSFAMQ
TENSPLFPPLLLSPDIIFNRIKNVRNFRRKSRTRSRSRSRSRSFSPENDYYKRSNYKYSR
SLHSSTVNSSEFDSSESDSSAYSSCRSSDYDSIRKFDNRISGQRYRNHRSSNYTYEEERK
VVYIGGLTEDVTKEDLRRNFLKYGTIKKISIHAKQDVNGNLRFGFITFAEASAAYDVLDK
FKLDSSLCDYDIRFGGRRRFCKQSYADLDSLPKEDDIDDVYNNNNININNTMKSKKAAEL
SFEELLNIARQKMCRNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g3376.t1 CDD cd00779 ProRS_core_prok 27 313 0.0000000
14 g3376.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 318 0.0000000
13 g3376.t1 Gene3D G3DSA:3.40.50.800 - 319 433 0.0000000
15 g3376.t1 Gene3D G3DSA:3.30.70.330 - 811 921 0.0000000
4 g3376.t1 PANTHER PTHR42753:SF2 PROLINE–TRNA LIGASE, MITOCHONDRIAL-RELATED 4 416 0.0000000
5 g3376.t1 PANTHER PTHR42753 MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER 4 416 0.0000000
8 g3376.t1 PRINTS PR01046 Prolyl-tRNA synthetase signature 76 94 0.0000000
7 g3376.t1 PRINTS PR01046 Prolyl-tRNA synthetase signature 112 123 0.0000000
6 g3376.t1 PRINTS PR01046 Prolyl-tRNA synthetase signature 143 151 0.0000000
9 g3376.t1 PRINTS PR01046 Prolyl-tRNA synthetase signature 153 164 0.0000000
1 g3376.t1 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 103 313 0.0000000
3 g3376.t1 Pfam PF03129 Anticodon binding domain 331 425 0.0000002
2 g3376.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 842 900 0.0000000
19 g3376.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 59 329 16.1310000
18 g3376.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 840 918 12.4070000
17 g3376.t1 SMART SM00360 rrm1_1 841 915 0.0000000
10 g3376.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 26 334 0.0000000
12 g3376.t1 SUPERFAMILY SSF52954 Class II aaRS ABD-related 320 428 0.0000000
11 g3376.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 789 900 0.0000000

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:0006433 prolyl-tRNA aminoacylation BP
GO:0005524 ATP binding MF
GO:0005737 cytoplasm CC
GO:0003676 nucleic acid binding MF
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0004827 proline-tRNA ligase activity 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