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.t8 TTS g5191.t8 7587382 7587382
chr_2 g5191 g5191.t8 isoform g5191.t8 7588392 7589913
chr_2 g5191 g5191.t8 exon g5191.t8.exon1 7588392 7589542
chr_2 g5191 g5191.t8 cds g5191.t8.CDS1 7588394 7589542
chr_2 g5191 g5191.t8 exon g5191.t8.exon2 7589656 7589913
chr_2 g5191 g5191.t8 cds g5191.t8.CDS2 7589656 7589913
chr_2 g5191 g5191.t8 TSS g5191.t8 7590003 7590003

Sequences

>g5191.t8 Gene=g5191 Length=1409
ATGACAGTAATTGTAAATCTCGTTAGACGTATAGTGAATTGTAGTGAAATCATCCTCAAA
CTCAATCAAAATCAAGTGAAACAGTGCGCACGAGATTTTTCAATCACAAGGAAATATTTT
AAAAACAATCAATTAGCTAATTGGGGTACCAAAAAGGCTCATCGTAATATAAAATTACAA
TTGCAATTGATACAAGAGATGGCCGATCCAAAAATTGAAGAGATACTTGCTCCATTAAGA
GCTGCTGTGAAAGAGCAAGGTGATTTGGTTCGACAACTAAAGAGCGATGGAGCACCTGAA
ATCGATGTTAAAAAAGCAATTGTTGAGTTGAAGGCTCGTAAAAAGATTCTTGAGGATAAA
GAATTAAGTTTGGCACCACAAGTTGCTTCATTTGATCGTGCAAAAATGGAAGATTTATTG
AAAAGACGATTCTTTTATGACCAAAGTTTTGCGATTTATGGAGGAATCACAGGTCAATAT
GATTTTGGTCCAATGGGATGCATGTTGAAAGCAAATATGCTTAATTTATGGCGTCAATTC
TTTGTACTCGAGGAACAAATGCTTGAAGTTGACTGCTCAATTCTTACACCTGAGCCTGTT
CTTAAAACAAGCGGACATGTTGATCGTTTTGCTGATTTGATGGTGAAAGATTCAAAGACT
GGTGAATGTTTCAGATTGGATCATTTGATTAAGGCACATTTAGAAAAGCTAGCATCTGAT
AAGAAAGCAACACAAGAATTGAAAGATGAATGTGCTGATATTGTGGTCAAATTGGATGGA
ATGAATAAACAAGAGATGGGAGATATTCTCAAAAAATTTAACATGAAATCTCCATTGACT
CAAAATGAGCTCACTGAGCCTATTGAATTCAATTTGATGTTTGGAACAAGCATCGGACCA
ACTGGTTTAGTTAAAGGATTTTTGAGACCAGAAACGGCTCAAGGAATTTTCGTAAACTTC
AAACGATTACTTGAATTTAATCAAGGAAGATTGCCTTTTGCAGCAGCTCAAATCGGAAAT
TCTTTTCGTAATGAAATTTCTCCACGTTCAGGATTGATTCGTGTGCGTGAATTTACAATG
GCTGAAATTGAACATTTTTGTGATCCCAATTTAAAGGATCATCCAAAATTCGTTGATGTC
GCTGATTATGAAATGACACTTTATTCGGCATGCAATCAAATGGATGGAAATAGTGCATCT
CGAATTACAATTGGAGAGGCTGTCAAAACTGGCTTGGTTGCTAATGAAACACTTGGTTAT
TTTATGGCACGCATTCAAATGTTCCTTATTAAAGTTGGTATTTTACCAGAACGTCTTCGT
TTTAGACAACATATGAATAATGAAATGGCACATTATGCGTGTGATTGTTGGGATGCAGAA
TGTTTGACAAGTTATGGATGGATCGAATG

>g5191.t8 Gene=g5191 Length=469
MTVIVNLVRRIVNCSEIILKLNQNQVKQCARDFSITRKYFKNNQLANWGTKKAHRNIKLQ
LQLIQEMADPKIEEILAPLRAAVKEQGDLVRQLKSDGAPEIDVKKAIVELKARKKILEDK
ELSLAPQVASFDRAKMEDLLKRRFFYDQSFAIYGGITGQYDFGPMGCMLKANMLNLWRQF
FVLEEQMLEVDCSILTPEPVLKTSGHVDRFADLMVKDSKTGECFRLDHLIKAHLEKLASD
KKATQELKDECADIVVKLDGMNKQEMGDILKKFNMKSPLTQNELTEPIEFNLMFGTSIGP
TGLVKGFLRPETAQGIFVNFKRLLEFNQGRLPFAAAQIGNSFRNEISPRSGLIRVREFTM
AEIEHFCDPNLKDHPKFVDVADYEMTLYSACNQMDGNSASRITIGEAVKTGLVANETLGY
FMARIQMFLIKVGILPERLRFRQHMNNEMAHYACDCWDAECLTSYGWIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5191.t8 CDD cd00935 GlyRS_RNA 76 126 3.88334E-25
16 g5191.t8 CDD cd00774 GlyRS-like_core 136 469 3.85914E-116
12 g5191.t8 Gene3D G3DSA:1.10.287.10 - 65 135 3.9E-7
13 g5191.t8 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 136 469 9.2E-169
14 g5191.t8 Gene3D G3DSA:1.20.1430.20 - 209 292 9.2E-169
3 g5191.t8 PANTHER PTHR10745:SF0 GLYCINE–TRNA LIGASE 130 469 1.1E-174
4 g5191.t8 PANTHER PTHR10745 GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2 130 469 1.1E-174
9 g5191.t8 PRINTS PR01043 Glycyl-tRNA synthetase signature 152 166 1.3E-38
6 g5191.t8 PRINTS PR01043 Glycyl-tRNA synthetase signature 288 300 1.3E-38
8 g5191.t8 PRINTS PR01043 Glycyl-tRNA synthetase signature 307 324 1.3E-38
7 g5191.t8 PRINTS PR01043 Glycyl-tRNA synthetase signature 339 356 1.3E-38
5 g5191.t8 PRINTS PR01043 Glycyl-tRNA synthetase signature 356 366 1.3E-38
2 g5191.t8 Pfam PF00458 WHEP-TRS domain 79 126 3.4E-10
1 g5191.t8 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 308 373 7.7E-10
17 g5191.t8 ProSitePatterns PS00762 WHEP-TRS domain signature. 86 114 -
20 g5191.t8 ProSiteProfiles PS51185 WHEP-TRS domain profile. 75 131 12.269
21 g5191.t8 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 264 366 8.817
18 g5191.t8 SMART SM00991 WHEP_TRS_a_2_a_3_a 79 134 7.1E-10
11 g5191.t8 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 78 118 1.53E-5
10 g5191.t8 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 133 469 7.85E-103
19 g5191.t8 TIGRFAM TIGR00389 glyS_dimeric: glycine–tRNA ligase 133 469 1.3E-133

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5191/g5191.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5191.t8.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

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