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_3 g3833 g3833.t4 TSS g3833.t4 28287301 28287301
chr_3 g3833 g3833.t4 isoform g3833.t4 28287380 28288522
chr_3 g3833 g3833.t4 exon g3833.t4.exon1 28287380 28287422
chr_3 g3833 g3833.t4 cds g3833.t4.CDS1 28287380 28287422
chr_3 g3833 g3833.t4 exon g3833.t4.exon2 28287528 28288203
chr_3 g3833 g3833.t4 cds g3833.t4.CDS2 28287528 28288203
chr_3 g3833 g3833.t4 exon g3833.t4.exon3 28288260 28288522
chr_3 g3833 g3833.t4 cds g3833.t4.CDS3 28288260 28288521
chr_3 g3833 g3833.t4 TTS g3833.t4 28289455 28289455

Sequences

>g3833.t4 Gene=g3833 Length=982
ATGCCAATTAAAGTAAATAGTGATTTAAAGAATCCACCAACCGATGGTGTGGATACCGCT
GAAAATTTTTCATCTCTTCCAAAAGACGCTAACTCTACAAAATCAAATAAACAAGAATCT
CCAACAGCACTTGATGTTGACGATAGAAAGCAAGAAGGTAAATTTGTCGATCTTCCAGGA
GCTGAAATGGGCAAAGTTATTGTTCGCTTTCCTCCTGAAGCATCAGGATATTTGCACATT
GGTCATGCTAAAGCAGCTCTTTTAAATCAATATTATCAACAAGCATTTAATGGAAAACTG
ATTATGAGATTTGACGACACTAATCCAGCTAAAGAAAATGTTCACTTTGAAAACGTTATT
TTAGAGGATTTAGAAATGCTTCAAATTAAACCAGATTTATTCACTTATACATCAGATTAT
TTTGAGCTCATGTTAAAGTATTGTGAACAATTAATGAAAGAGAGAAAAGCATATGCTGAC
GATACTGATCCTGAACTGATGAAGCAAGAACGTGAACAGAGAGTTGAGTCTAAAAACAGA
AACAACTCAATCGAAAAGAATTTTGAAATGTGGAATGAAATGTTAGCTGGCACAGAAAAA
GGACAGAAATGTTGTATCCGAGCGAAAATCGACATGTCTTCTCCAAATGGATGCCTTCGT
GATCCAACAATTTATCGTTGCAAAAATGAGCCACATCCACGTACTGGAACTAAATACAAA
GTTTATCCAACTTATGATTTTGCATGTCCAATTGTTGATGCAATTGAAAATGTAACTCAT
ACTCTTCGTACAATGGAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCA
TTAAAACTTCGTAAACCATATATTTGGGAATATTCTCGTTTAAATATGACTAACACAGTA
TTATCAAAACGTAAATTAACTTGGTTTGTTGAAAACGGTCTTGTTGATGGTTGGGATGAT
CCTCGCTTTCCTACAGTTCGAG

>g3833.t4 Gene=g3833 Length=327
MPIKVNSDLKNPPTDGVDTAENFSSLPKDANSTKSNKQESPTALDVDDRKQEGKFVDLPG
AEMGKVIVRFPPEASGYLHIGHAKAALLNQYYQQAFNGKLIMRFDDTNPAKENVHFENVI
LEDLEMLQIKPDLFTYTSDYFELMLKYCEQLMKERKAYADDTDPELMKQEREQRVESKNR
NNSIEKNFEMWNEMLAGTEKGQKCCIRAKIDMSSPNGCLRDPTIYRCKNEPHPRTGTKYK
VYPTYDFACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDALKLRKPYIWEYSRLNMTNTV
LSKRKLTWFVENGLVDGWDDPRFPTVR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3833.t4 Coils Coil Coil 167 187 -
9 g3833.t4 Gene3D G3DSA:3.40.50.620 HUPs 33 327 1.4E-112
13 g3833.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 51 -
12 g3833.t4 MobiDBLite mobidb-lite consensus disorder prediction 17 40 -
2 g3833.t4 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 35 327 1.1E-187
4 g3833.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 69 81 2.5E-18
7 g3833.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 83 94 2.5E-18
6 g3833.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 98 111 2.5E-18
3 g3833.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 243 253 2.5E-18
5 g3833.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 259 267 2.5E-18
1 g3833.t4 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 65 326 4.6E-105
11 g3833.t4 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 72 83 -
8 g3833.t4 SUPERFAMILY SSF52374 Nucleotidylyl transferase 65 317 1.31E-75

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:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0043039 tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed