Gene loci information

Transcript annotation

  • This transcript has been annotated as Bifunctional glutamate/proline–tRNA ligase.

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_4 g17015 g17015.t9 TSS g17015.t9 12156272 12156272
chr_4 g17015 g17015.t9 isoform g17015.t9 12156363 12161626
chr_4 g17015 g17015.t9 exon g17015.t9.exon1 12156363 12156405
chr_4 g17015 g17015.t9 cds g17015.t9.CDS1 12156363 12156405
chr_4 g17015 g17015.t9 exon g17015.t9.exon2 12156511 12157603
chr_4 g17015 g17015.t9 cds g17015.t9.CDS2 12156511 12157603
chr_4 g17015 g17015.t9 exon g17015.t9.exon3 12157660 12157922
chr_4 g17015 g17015.t9 cds g17015.t9.CDS3 12157660 12157922
chr_4 g17015 g17015.t9 exon g17015.t9.exon4 12160076 12160863
chr_4 g17015 g17015.t9 cds g17015.t9.CDS4 12160076 12160863
chr_4 g17015 g17015.t9 exon g17015.t9.exon5 12160967 12161626
chr_4 g17015 g17015.t9 cds g17015.t9.CDS5 12160967 12160981
chr_4 g17015 g17015.t9 TTS g17015.t9 NA NA

Sequences

>g17015.t9 Gene=g17015 Length=2847
ATGCCAATCAAAGTAATTTGTGATTTAAAGAATCCACCAATTGGTGCTTTGGTTGTTGCC
GAAATTATTAAATCAACTGATCCAGTTGTAATTGAATGGAGCGATAAAGAAGCATCTATC
AATTTTGGTAACAATTCACTTTCATGTGTGAGCAACAACGACCTTTTAAGAGCTCTAGCT
CGACAAGCCGGAAGTTATCAGCTTTATGGAAAAACTCCGATTGAAAGAACTCAAATTGAT
CATTGGTTGACTTACTGCCTCAATTATGATGCTCATATTGATGAAGCAATTCAATATTTG
AATAAATGTTTAGCTCCATTGACTTATTTAGTGTCAAATAAGCTGACAATTGCTGATTTA
GCTGTGTTCAATGAATTTTTTGTCAAGTATGATCTTTTGAAGAAATCTGGTTTGCCTAGT
CATGTTCAACGCTGGTATAACCTCATCAGTTCATTGCCAACAGTTCAAACTGTGCTTTCA
TCACTTCCAAAAGATGGTAAATCTACAAAATCAAAGAAACAAGAAAAACAAGAATTTTCA
GCAGCTCTTGGTGTTGGCGATAGAAAGCAAGAAGGAAAATTTGTCGATCTTCCAGGAGCT
GAAATGGGAAAAGTTGTTGTTCGCTTTCCTCCTGAAGCATCAGGGTATTTGCACATTGGT
CATGCTAAAGCAGCTCTTTTAAATCAATATTATCAGCAAGCATTTGATGGAAAATTGATT
ATGAGATTTGATGACACCAATCCAGCTAAAGAAAATGTTCATTTTGAGGAAGTCATTTTG
GAAGATGTAGAAATGCTTCAAATTAAACCTGATGCATTCACTTACACCTCAGATTATTTT
GATATCATGCTTAAATATTGTGAGCAATTAATGAAAGAAGGAAAAGCATATGCTGATGAT
ACTGATCCTGAATTGATGAAACAAGAACGTGAACAGAAAGTTGAGTCAAAGAACCGAAAT
AATTCGGTTGAAAAGAATTTTGAAATGTGGAAAGAAATGTTGGCTGGCACAGAAAAAGGA
CAAAAATGTTGTATTCGAGCAAAAATTGACATGTCATCACCAAATGGATGCCTTCGTGAT
CCAACAATTTATCGTTGCAAAAATGAACCACATCCACGTACTGGAACTAATTACAAAGTT
TATCCAACTTATGATTTTGCTTGTCCTATTGTTGATGCAATTGAAAATGTGACTCATACT
CTTCGTACAATGGAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCATTG
AAACTTCGTAAACCATACATTTGGGAATATTCACGTTTAAATATGACTAACACTGTTCTA
TCTAAACGTAAATTGACTTGGTTTGTTGAAAACGGTCTGGTTGATGGCTGGGATGATCCT
CGTTTTCCTACAGTTCGAGGTGTTTTACGTCGTGGTATGACTGTTGAAGGTCTAAAACAA
TTCATTATTGCACAAGGTTCTAGTAAAGCTGTAGTATTTATGGAATGGGATAAAATTTGG
GCTTTCAATAAGAAAGTCATTGATCCAATTGCACCTAGATATACAGCATTAGAAAATGAC
AATCGTATTATTGTTAAAGTCGCTAATGCAAAATTGCAAGCACTTGAAGTTCCAAAACAT
CCCAAAAATGAGGAAGTTGGCACAAAAACTATTTGGGTTGGTCCAGAAATTTATATTGAC
TATGCTGATGCTGAATGTTTAAAAGAAGGTGAAAATGCGACATTTATAAATTGGGGTAAT
TTGAGAATCAAGAAAATTCATAAAGAAGGAGAAAAAATTACTTCAGTCGATGCTGAATTG
AATTTGGGTGACACTGATTTCAAAAAGACGTTAAAACTTACATGGCTTTGTAAACAAGAT
CCATCAGAATATCCACCAACTTATTGTGTTTATTTTGATCATATTATAAACAAATCTGTT
CTTGGTAAAGATGAAGACTTTAAATCATACATCGGACATGAGACTAGAAAAGAAACAAAA
ATGTTTGGTGATCCTGAATTGAAAAAATGTCAAAAAGGCGACATCATTCAACTACAACGA
CGTGGATTTTTCAAAGTTGATCAAGCTTATGCTCCAGCTAGTGAAATTTCAGGAGTTGAA
CGTCCAATTGTTTTGTTCTTTATTCCTGATGGTCATAAAAAAGAAATGCCCACGTCTGGT
CTTTCAAAGAAACTTCAAGCAGCAGAGAAAAAATTACTATAAAAGCTCTTCATTGTACAC
ACATTGAAAGTTTTATCTTTTTTTACAATGAGTGAATGTAGTAGTTTTAATTCATCAATG
TGATCGCTTTTGCCACATTGTAAATTTCATGCTCAAAGAGTTTTTGAATTAAATTAATCA
AAATTATCCAAAATTCTAGGAAAAATCAAACAACAGTGCATCAGTGATTAAAAAATCATC
ATCTGTTGGACAAGTAAGTGACATTAATGAAAAAATAAACAAACAAGGTGACGTTGTAAG
AAATTTGAAGAGCCAAAAGGCAGCAAAGCAAGACATTGACGCAGCAGTAAAAATTCTATT
GGAATTAAAAGCAGAATATAAAACAGCAACTGGTCAAGATTGGAAACCAGGTGCTACTCC
TGTTAAAACTGAAACAAAATCTACTCCATCAATCGGGCAAGTCAGTGACATTAACGAAAA
AATTGTTCAGCAAGGCGACATTGTCAGAAATTTGAAGAGCCAAAAGGCAGCAAAGCAAGA
CATTGACGCAGCAGTGAAAATTCTGTTAGAATTAAAAGCAGAATATAAAACAGCAACTGG
TCAAGATTGGAAACCAGGTGCTACTCCTGTTAAAACTGAAACAAAAGCTGCTCCATCAGT
TGGACAAGTCAGTGACATCAATGAAAA

>g17015.t9 Gene=g17015 Length=733
MPIKVICDLKNPPIGALVVAEIIKSTDPVVIEWSDKEASINFGNNSLSCVSNNDLLRALA
RQAGSYQLYGKTPIERTQIDHWLTYCLNYDAHIDEAIQYLNKCLAPLTYLVSNKLTIADL
AVFNEFFVKYDLLKKSGLPSHVQRWYNLISSLPTVQTVLSSLPKDGKSTKSKKQEKQEFS
AALGVGDRKQEGKFVDLPGAEMGKVVVRFPPEASGYLHIGHAKAALLNQYYQQAFDGKLI
MRFDDTNPAKENVHFEEVILEDVEMLQIKPDAFTYTSDYFDIMLKYCEQLMKEGKAYADD
TDPELMKQEREQKVESKNRNNSVEKNFEMWKEMLAGTEKGQKCCIRAKIDMSSPNGCLRD
PTIYRCKNEPHPRTGTNYKVYPTYDFACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDAL
KLRKPYIWEYSRLNMTNTVLSKRKLTWFVENGLVDGWDDPRFPTVRGVLRRGMTVEGLKQ
FIIAQGSSKAVVFMEWDKIWAFNKKVIDPIAPRYTALENDNRIIVKVANAKLQALEVPKH
PKNEEVGTKTIWVGPEIYIDYADAECLKEGENATFINWGNLRIKKIHKEGEKITSVDAEL
NLGDTDFKKTLKLTWLCKQDPSEYPPTYCVYFDHIINKSVLGKDEDFKSYIGHETRKETK
MFGDPELKKCQKGDIIQLQRRGFFKVDQAYAPASEISGVERPIVLFFIPDGHKKEMPTSG
LSKKLQAAEKKLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g17015.t9 CDD cd00807 GlnRS_core 204 513 4.33431E-141
18 g17015.t9 Coils Coil Coil 306 326 -
17 g17015.t9 Gene3D G3DSA:1.20.1050.130 - 1 170 1.9E-39
14 g17015.t9 Gene3D G3DSA:3.40.50.620 HUPs 177 513 4.3E-131
16 g17015.t9 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 514 690 5.0E-23
15 g17015.t9 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 519 621 5.0E-23
5 g17015.t9 Hamap MF_02076 Glutamate–tRNA ligase [gltX]. 106 708 31.802025
4 g17015.t9 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 15 730 0.0
8 g17015.t9 PRINTS PR00987 Glutamyl-tRNA synthetase signature 208 220 8.4E-17
7 g17015.t9 PRINTS PR00987 Glutamyl-tRNA synthetase signature 222 233 8.4E-17
10 g17015.t9 PRINTS PR00987 Glutamyl-tRNA synthetase signature 237 250 8.4E-17
6 g17015.t9 PRINTS PR00987 Glutamyl-tRNA synthetase signature 382 392 8.4E-17
9 g17015.t9 PRINTS PR00987 Glutamyl-tRNA synthetase signature 398 406 8.4E-17
2 g17015.t9 Pfam PF14497 Glutathione S-transferase, C-terminal domain 91 161 1.7E-4
1 g17015.t9 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 204 508 7.6E-119
3 g17015.t9 Pfam PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain 511 687 9.9E-32
20 g17015.t9 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 211 222 -
13 g17015.t9 SUPERFAMILY SSF47616 GST C-terminal domain-like 54 157 3.76E-16
11 g17015.t9 SUPERFAMILY SSF52374 Nucleotidylyl transferase 204 516 1.42E-85
12 g17015.t9 SUPERFAMILY SSF50715 Ribosomal protein L25-like 511 713 2.3E-44
21 g17015.t9 TIGRFAM TIGR00463 gltX_arch: glutamate–tRNA ligase 168 690 4.7E-154

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:0005524 ATP binding MF
GO:0005737 cytoplasm CC
GO:0004818 glutamate-tRNA ligase activity MF
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0043039 tRNA aminoacylation BP
GO:0006412 translation BP
GO:0006424 glutamyl-tRNA aminoacylation BP
GO:0004812 aminoacyl-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