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.t8 TTS g3376.t8 24964235 24964235
chr_3 g3376 g3376.t8 isoform g3376.t8 24964293 24965519
chr_3 g3376 g3376.t8 exon g3376.t8.exon1 24964293 24965210
chr_3 g3376 g3376.t8 cds g3376.t8.CDS1 24964293 24965210
chr_3 g3376 g3376.t8 exon g3376.t8.exon2 24965266 24965519
chr_3 g3376 g3376.t8 cds g3376.t8.CDS2 24965266 24965514
chr_3 g3376 g3376.t8 TSS g3376.t8 24965667 24965667

Sequences

>g3376.t8 Gene=g3376 Length=1172
AGTTAATGATAGATTGCGGTTTAATAAAACATTGCAATAATGGAACATATTACATATTAC
CTTTACTACAAAGATCAATTGAGAAATTAACAAAAATCATTGATCATTATATGACAGAAA
TCGATGGTCAAAAAATTACTATGCCCACATTAACATCAGCAGACTTATGGAAAAAATCTG
GGAGATTTGAAAATGCAGTAACTGAATTGATGACAGTCAATGATAGGCATAATAGACTTC
AAATTCTTAGTCCTACACATGAGGAATCAGTGACAAACTTAATTGCATCTATTTCTCCAG
TCTCTTACAAAAGCTTTCCTCTTCGTCTTTATCAAATTACACCTAAATTTCGAGATGAGT
TAAGACCAAAATTTGGATTATTGAGAGCAAAAGAGTTTTTAATGAAGGATATGTACACCT
TTGATATTGGATTAAATGAGGCTAAAAAGACATATGATGAAGTTAATGAACAATATGTCA
AAATTTTCAATCATTTGAATGTATCCTTTATAAAAATTGGCGCTGATACTGGTAATATGG
GCGGAAATATTTCTCATGAATTTCATATAGCAAGTTCTATTGGCGAAGATTCAATCATTT
CATGTACATCTTGTTCAAAAGCTATTAATGTTGAATTGGCAAAAGATGGAAAAATATGTG
AACAATGTAAAATTGATGATCTTAAACGTCAGCAAGGAATTGAAATTGGTCACACATTTA
TTCTTGAAGATAGGTATTCAAAAGTGTTAAATGCTACATTTTTAAATAAAACTGGAAAAC
CAGAAAATATTCAAATGGGTTGTTATGGAATCGGTGTGACTCGTCTTATAGCAGCAGTAA
TTGAACTTTTCTCAAACGAAAATGAAATCAGATGGTCAGATGCAATAGCACCATACAAAA
TTTGTATTATTCCACCAAAGGAAGGAAGCAAAGAAGAGGAGTCTGTTAAGCATTTAAGCA
ATGAAATTTATCATTATCTGACTACTAATTCATCACAACTTGCGGATGATATTATTGTAG
ATGATCGAACACACATGACAATTGGTAAACGGTTGAAAGAGATCAAGAAACTTGGAATAC
CTTATATTATAGTTATTGGATCAAAATCAGCTGATATAAGTTCTACAATAGAAGTTCATA
ATTTGAGAGAAAATGTAGCCATAGATATGAGT

>g3376.t8 Gene=g3376 Length=389
MIDCGLIKHCNNGTYYILPLLQRSIEKLTKIIDHYMTEIDGQKITMPTLTSADLWKKSGR
FENAVTELMTVNDRHNRLQILSPTHEESVTNLIASISPVSYKSFPLRLYQITPKFRDELR
PKFGLLRAKEFLMKDMYTFDIGLNEAKKTYDEVNEQYVKIFNHLNVSFIKIGADTGNMGG
NISHEFHIASSIGEDSIISCTSCSKAINVELAKDGKICEQCKIDDLKRQQGIEIGHTFIL
EDRYSKVLNATFLNKTGKPENIQMGCYGIGVTRLIAAVIELFSNENEIRWSDAIAPYKIC
IIPPKEGSKEEESVKHLSNEIYHYLTTNSSQLADDIIVDDRTHMTIGKRLKEIKKLGIPY
IIVIGSKSADISSTIEVHNLRENVAIDMS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g3376.t8 CDD cd00779 ProRS_core_prok 1 280 0.0000000
12 g3376.t8 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 285 0.0000000
11 g3376.t8 Gene3D G3DSA:3.40.50.800 - 286 389 0.0000000
3 g3376.t8 PANTHER PTHR42753:SF2 PROLINE–TRNA LIGASE, MITOCHONDRIAL-RELATED 1 381 0.0000000
4 g3376.t8 PANTHER PTHR42753 MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER 1 381 0.0000000
5 g3376.t8 PRINTS PR01046 Prolyl-tRNA synthetase signature 43 61 0.0000000
7 g3376.t8 PRINTS PR01046 Prolyl-tRNA synthetase signature 79 90 0.0000000
8 g3376.t8 PRINTS PR01046 Prolyl-tRNA synthetase signature 110 118 0.0000000
6 g3376.t8 PRINTS PR01046 Prolyl-tRNA synthetase signature 120 131 0.0000000
1 g3376.t8 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 70 280 0.0000000
2 g3376.t8 Pfam PF03129 Anticodon binding domain 298 381 0.0000003
13 g3376.t8 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 26 296 16.1310000
9 g3376.t8 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 2 301 0.0000000
10 g3376.t8 SUPERFAMILY SSF52954 Class II aaRS ABD-related 287 369 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:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005737 cytoplasm CC
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