Gene loci information

Transcript annotation

  • This transcript has been annotated as Glycine–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_2 g5191 g5191.t4 TTS g5191.t4 7587382 7587382
chr_2 g5191 g5191.t4 isoform g5191.t4 7587510 7588392
chr_2 g5191 g5191.t4 exon g5191.t4.exon1 7587510 7587808
chr_2 g5191 g5191.t4 cds g5191.t4.CDS1 7587510 7587808
chr_2 g5191 g5191.t4 exon g5191.t4.exon2 7587862 7588392
chr_2 g5191 g5191.t4 cds g5191.t4.CDS2 7587862 7588264
chr_2 g5191 g5191.t4 TSS g5191.t4 NA NA

Sequences

>g5191.t4 Gene=g5191 Length=830
GTGTTGGTTGTGCTGATCGTTCTGCTTATGATTTAACTCAGCATACAAATGCAACAGGTG
TCAGGCTTACTGCTGAGAAAAAGTTACCAGAGCCTAAAACTATTGAATTCACAGAAGCAG
TTCCTAATATGAAAATTTTAGGAAAATTATTCAAGAAAGACGCAAAGGAGATTACAGAAC
TTCTTTCAAAATTATCAATTGATGATCTTAAAAAAATGAATGATGAGCTTACACAAAATA
ATTCTTACACATTGAAATCAGATGCAAACTCATATACTCTTAATAATGAGATGGTAACCA
TCAAATCTGGATCTAAGACAATTCATGTTGAGGAAATTATTCCATCAGTTATTGAACCGT
CATTTGGAATTGGAAGAATTATGTATGCGCTTTTGGAGCATCGTTTCCAAATGAGAGATG
GAGATGAGCAACGTTGTTTCTTCTCACTTCCACCTATTGTTGCACCTCTTAAATGCTCTG
TTTTGCCGCTCAGTAATAATCAAGAATTTACACCATTCATCAAACAGATTTCTTCTGCTT
TGACGCGAGTTGATGTTTCGCATAAGGTTGATGATTCAAGTGGGTCAATTGGTCGCCGTT
ATGCACGTACTGATGAAATTGCAATTGCTTATGGCATCACAATCGATTTTGATACTGTCA
AAGACAAAACTGTAACACTTCGTGAAAGAGACTCAATGACACAAATTAGAATCCCGATAG
ATGAAGTTGCAGAAGTTGTGAGAAATCTTTCATACAGTAAAATCGAATGGTCTGACGTTA
CCTCAAAATATCCCAAGTTTGAACAACAAGAAAATGCAGCACAAAAGTAA

>g5191.t4 Gene=g5191 Length=233
MKILGKLFKKDAKEITELLSKLSIDDLKKMNDELTQNNSYTLKSDANSYTLNNEMVTIKS
GSKTIHVEEIIPSVIEPSFGIGRIMYALLEHRFQMRDGDEQRCFFSLPPIVAPLKCSVLP
LSNNQEFTPFIKQISSALTRVDVSHKVDDSSGSIGRRYARTDEIAIAYGITIDFDTVKDK
TVTLRERDSMTQIRIPIDEVAEVVRNLSYSKIEWSDVTSKYPKFEQQENAAQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5191.t4 CDD cd00858 GlyRS_anticodon 88 209 5.13763E-62
10 g5191.t4 Coils Coil Coil 221 233 -
9 g5191.t4 Gene3D G3DSA:1.10.30.30 - 2 63 2.9E-15
8 g5191.t4 Gene3D G3DSA:3.40.50.800 - 113 228 8.4E-44
2 g5191.t4 PANTHER PTHR10745:SF0 GLYCINE–TRNA LIGASE 2 223 2.2E-82
3 g5191.t4 PANTHER PTHR10745 GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2 2 223 2.2E-82
4 g5191.t4 PRINTS PR01043 Glycyl-tRNA synthetase signature 72 84 1.0E-12
5 g5191.t4 PRINTS PR01043 Glycyl-tRNA synthetase signature 154 173 1.0E-12
1 g5191.t4 Pfam PF03129 Anticodon binding domain 115 206 2.9E-24
6 g5191.t4 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 19 118 4.28E-9
7 g5191.t4 SUPERFAMILY SSF52954 Class II aaRS ABD-related 102 224 1.39E-35

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5191/g5191.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5191.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004820 glycine-tRNA ligase activity MF
GO:0005524 ATP binding MF
GO:0006426 glycyl-tRNA aminoacylation BP
GO:0000166 nucleotide binding MF
GO:0005737 cytoplasm CC

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.

Raw TPM values