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.t5 TTS g5191.t5 7587382 7587382
chr_2 g5191 g5191.t5 isoform g5191.t5 7587510 7589913
chr_2 g5191 g5191.t5 exon g5191.t5.exon1 7587510 7587808
chr_2 g5191 g5191.t5 cds g5191.t5.CDS1 7587510 7587808
chr_2 g5191 g5191.t5 exon g5191.t5.exon2 7587862 7589542
chr_2 g5191 g5191.t5 cds g5191.t5.CDS2 7587862 7589395
chr_2 g5191 g5191.t5 exon g5191.t5.exon3 7589652 7589913
chr_2 g5191 g5191.t5 TSS g5191.t5 7590003 7590003

Sequences

>g5191.t5 Gene=g5191 Length=2242
ATGACAGTAATTGTAAATCTCGTTAGACGTATAGTGAATTGTAGTGAAATCATCCTCAAA
CTCAATCAAAATCAAGTGAAACAGTGCGCACGAGATTTTTCAATCACAAGGAAATATTTT
AAAAACAATCAATTAGCTAATTGGGGTACCAAAAAGGCTCATCGTAATATAAAATTACAA
TTGCAATTGATACAAGAGATGGCCGATCCAAAAATTGAAGAGATACTTGCTCCATTAAGA
GCTGCTGTGAAAGAGCAAGTAAGGTGATTTGGTTCGACAACTAAAGAGCGATGGAGCACC
TGAAATCGATGTTAAAAAAGCAATTGTTGAGTTGAAGGCTCGTAAAAAGATTCTTGAGGA
TAAAGAATTAAGTTTGGCACCACAAGTTGCTTCATTTGATCGTGCAAAAATGGAAGATTT
ATTGAAAAGACGATTCTTTTATGACCAAAGTTTTGCGATTTATGGAGGAATCACAGGTCA
ATATGATTTTGGTCCAATGGGATGCATGTTGAAAGCAAATATGCTTAATTTATGGCGTCA
ATTCTTTGTACTCGAGGAACAAATGCTTGAAGTTGACTGCTCAATTCTTACACCTGAGCC
TGTTCTTAAAACAAGCGGACATGTTGATCGTTTTGCTGATTTGATGGTGAAAGATTCAAA
GACTGGTGAATGTTTCAGATTGGATCATTTGATTAAGGCACATTTAGAAAAGCTAGCATC
TGATAAGAAAGCAACACAAGAATTGAAAGATGAATGTGCTGATATTGTGGTCAAATTGGA
TGGAATGAATAAACAAGAGATGGGAGATATTCTCAAAAAATTTAACATGAAATCTCCATT
GACTCAAAATGAGCTCACTGAGCCTATTGAATTCAATTTGATGTTTGGAACAAGCATCGG
ACCAACTGGTTTAGTTAAAGGATTTTTGAGACCAGAAACGGCTCAAGGAATTTTCGTAAA
CTTCAAACGATTACTTGAATTTAATCAAGGAAGATTGCCTTTTGCAGCAGCTCAAATCGG
AAATTCTTTTCGTAATGAAATTTCTCCACGTTCAGGATTGATTCGTGTGCGTGAATTTAC
AATGGCTGAAATTGAACATTTTTGTGATCCCAATTTAAAGGATCATCCAAAATTCGTTGA
TGTCGCTGATTATGAAATGACACTTTATTCGGCATGCAATCAAATGGATGGAAATAGTGC
ATCTCGAATTACAATTGGAGAGGCTGTCAAAACTGGCTTGGTTGCTAATGAAACACTTGG
TTATTTTATGGCACGCATTCAAATGTTCCTTATTAAAGTTGGTATTTTACCAGAACGTCT
TCGTTTTAGACAACATATGAATAATGAAATGGCACATTATGCGTGTGATTGTTGGGATGC
AGAATGTTTGACAAGTTATGGATGGATCGAATGTGTTGGTTGTGCTGATCGTTCTGCTTA
TGATTTAACTCAGCATACAAATGCAACAGGTGTCAGGCTTACTGCTGAGAAAAAGTTACC
AGAGCCTAAAACTATTGAATTCACAGAAGCAGTTCCTAATATGAAAATTTTAGGAAAATT
ATTCAAGAAAGACGCAAAGGAGATTACAGAACTTCTTTCAAAATTATCAATTGATGATCT
TAAAAAAATGAATGATGAGCTTACACAAAATAATTCTTACACATTGAAATCAGATGCAAA
CTCATATACTCTTAATAATGAGATGGTAACCATCAAATCTGGATCTAAGACAATTCATGT
TGAGGAAATTATTCCATCAGTTATTGAACCGTCATTTGGAATTGGAAGAATTATGTATGC
GCTTTTGGAGCATCGTTTCCAAATGAGAGATGGAGATGAGCAACGTTGTTTCTTCTCACT
TCCACCTATTGTTGCACCTCTTAAATGCTCTGTTTTGCCGCTCAGTAATAATCAAGAATT
TACACCATTCATCAAACAGATTTCTTCTGCTTTGACGCGAGTTGATGTTTCGCATAAGGT
TGATGATTCAAGTGGGTCAATTGGTCGCCGTTATGCACGTACTGATGAAATTGCAATTGC
TTATGGCATCACAATCGATTTTGATACTGTCAAAGACAAAACTGTAACACTTCGTGAAAG
AGACTCAATGACACAAATTAGAATCCCGATAGATGAAGTTGCAGAAGTTGTGAGAAATCT
TTCATACAGTAAAATCGAATGGTCTGACGTTACCTCAAAATATCCCAAGTTTGAACAACA
AGAAAATGCAGCACAAAAGTAA

>g5191.t5 Gene=g5191 Length=610
MEDLLKRRFFYDQSFAIYGGITGQYDFGPMGCMLKANMLNLWRQFFVLEEQMLEVDCSIL
TPEPVLKTSGHVDRFADLMVKDSKTGECFRLDHLIKAHLEKLASDKKATQELKDECADIV
VKLDGMNKQEMGDILKKFNMKSPLTQNELTEPIEFNLMFGTSIGPTGLVKGFLRPETAQG
IFVNFKRLLEFNQGRLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFCDPNLKDHP
KFVDVADYEMTLYSACNQMDGNSASRITIGEAVKTGLVANETLGYFMARIQMFLIKVGIL
PERLRFRQHMNNEMAHYACDCWDAECLTSYGWIECVGCADRSAYDLTQHTNATGVRLTAE
KKLPEPKTIEFTEAVPNMKILGKLFKKDAKEITELLSKLSIDDLKKMNDELTQNNSYTLK
SDANSYTLNNEMVTIKSGSKTIHVEEIIPSVIEPSFGIGRIMYALLEHRFQMRDGDEQRC
FFSLPPIVAPLKCSVLPLSNNQEFTPFIKQISSALTRVDVSHKVDDSSGSIGRRYARTDE
IAIAYGITIDFDTVKDKTVTLRERDSMTQIRIPIDEVAEVVRNLSYSKIEWSDVTSKYPK
FEQQENAAQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5191.t5 CDD cd00774 GlyRS-like_core 1 347 0.00
18 g5191.t5 CDD cd00858 GlyRS_anticodon 465 586 0.00
15 g5191.t5 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 4 477 0.00
17 g5191.t5 Gene3D G3DSA:1.20.1430.20 - 75 158 0.00
16 g5191.t5 Gene3D G3DSA:1.10.30.30 - 363 440 0.00
14 g5191.t5 Gene3D G3DSA:3.40.50.800 - 490 605 0.00
3 g5191.t5 PANTHER PTHR10745:SF0 GLYCINE–TRNA LIGASE 1 600 0.00
4 g5191.t5 PANTHER PTHR10745 GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2 1 600 0.00
8 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 17 31 0.00
11 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 153 165 0.00
5 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 172 189 0.00
10 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 204 221 0.00
7 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 221 231 0.00
9 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 449 461 0.00
6 g5191.t5 PRINTS PR01043 Glycyl-tRNA synthetase signature 531 550 0.00
1 g5191.t5 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 173 238 0.00
2 g5191.t5 Pfam PF03129 Anticodon binding domain 492 583 0.00
20 g5191.t5 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 129 490 10.33
12 g5191.t5 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 2 495 0.00
13 g5191.t5 SUPERFAMILY SSF52954 Class II aaRS ABD-related 479 601 0.00
21 g5191.t5 TIGRFAM TIGR00389 glyS_dimeric: glycine–tRNA ligase 2 583 0.00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5191/g5191.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5191.t5.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:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005737 cytoplasm CC

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