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.t1 TTS g5191.t1 7587382 7587382
chr_2 g5191 g5191.t1 isoform g5191.t1 7587510 7589913
chr_2 g5191 g5191.t1 exon g5191.t1.exon1 7587510 7587808
chr_2 g5191 g5191.t1 cds g5191.t1.CDS1 7587510 7587808
chr_2 g5191 g5191.t1 exon g5191.t1.exon2 7587862 7589542
chr_2 g5191 g5191.t1 cds g5191.t1.CDS2 7587862 7589542
chr_2 g5191 g5191.t1 exon g5191.t1.exon3 7589656 7589913
chr_2 g5191 g5191.t1 cds g5191.t1.CDS3 7589656 7589913
chr_2 g5191 g5191.t1 TSS g5191.t1 7590003 7590003

Sequences

>g5191.t1 Gene=g5191 Length=2238
ATGACAGTAATTGTAAATCTCGTTAGACGTATAGTGAATTGTAGTGAAATCATCCTCAAA
CTCAATCAAAATCAAGTGAAACAGTGCGCACGAGATTTTTCAATCACAAGGAAATATTTT
AAAAACAATCAATTAGCTAATTGGGGTACCAAAAAGGCTCATCGTAATATAAAATTACAA
TTGCAATTGATACAAGAGATGGCCGATCCAAAAATTGAAGAGATACTTGCTCCATTAAGA
GCTGCTGTGAAAGAGCAAGGTGATTTGGTTCGACAACTAAAGAGCGATGGAGCACCTGAA
ATCGATGTTAAAAAAGCAATTGTTGAGTTGAAGGCTCGTAAAAAGATTCTTGAGGATAAA
GAATTAAGTTTGGCACCACAAGTTGCTTCATTTGATCGTGCAAAAATGGAAGATTTATTG
AAAAGACGATTCTTTTATGACCAAAGTTTTGCGATTTATGGAGGAATCACAGGTCAATAT
GATTTTGGTCCAATGGGATGCATGTTGAAAGCAAATATGCTTAATTTATGGCGTCAATTC
TTTGTACTCGAGGAACAAATGCTTGAAGTTGACTGCTCAATTCTTACACCTGAGCCTGTT
CTTAAAACAAGCGGACATGTTGATCGTTTTGCTGATTTGATGGTGAAAGATTCAAAGACT
GGTGAATGTTTCAGATTGGATCATTTGATTAAGGCACATTTAGAAAAGCTAGCATCTGAT
AAGAAAGCAACACAAGAATTGAAAGATGAATGTGCTGATATTGTGGTCAAATTGGATGGA
ATGAATAAACAAGAGATGGGAGATATTCTCAAAAAATTTAACATGAAATCTCCATTGACT
CAAAATGAGCTCACTGAGCCTATTGAATTCAATTTGATGTTTGGAACAAGCATCGGACCA
ACTGGTTTAGTTAAAGGATTTTTGAGACCAGAAACGGCTCAAGGAATTTTCGTAAACTTC
AAACGATTACTTGAATTTAATCAAGGAAGATTGCCTTTTGCAGCAGCTCAAATCGGAAAT
TCTTTTCGTAATGAAATTTCTCCACGTTCAGGATTGATTCGTGTGCGTGAATTTACAATG
GCTGAAATTGAACATTTTTGTGATCCCAATTTAAAGGATCATCCAAAATTCGTTGATGTC
GCTGATTATGAAATGACACTTTATTCGGCATGCAATCAAATGGATGGAAATAGTGCATCT
CGAATTACAATTGGAGAGGCTGTCAAAACTGGCTTGGTTGCTAATGAAACACTTGGTTAT
TTTATGGCACGCATTCAAATGTTCCTTATTAAAGTTGGTATTTTACCAGAACGTCTTCGT
TTTAGACAACATATGAATAATGAAATGGCACATTATGCGTGTGATTGTTGGGATGCAGAA
TGTTTGACAAGTTATGGATGGATCGAATGTGTTGGTTGTGCTGATCGTTCTGCTTATGAT
TTAACTCAGCATACAAATGCAACAGGTGTCAGGCTTACTGCTGAGAAAAAGTTACCAGAG
CCTAAAACTATTGAATTCACAGAAGCAGTTCCTAATATGAAAATTTTAGGAAAATTATTC
AAGAAAGACGCAAAGGAGATTACAGAACTTCTTTCAAAATTATCAATTGATGATCTTAAA
AAAATGAATGATGAGCTTACACAAAATAATTCTTACACATTGAAATCAGATGCAAACTCA
TATACTCTTAATAATGAGATGGTAACCATCAAATCTGGATCTAAGACAATTCATGTTGAG
GAAATTATTCCATCAGTTATTGAACCGTCATTTGGAATTGGAAGAATTATGTATGCGCTT
TTGGAGCATCGTTTCCAAATGAGAGATGGAGATGAGCAACGTTGTTTCTTCTCACTTCCA
CCTATTGTTGCACCTCTTAAATGCTCTGTTTTGCCGCTCAGTAATAATCAAGAATTTACA
CCATTCATCAAACAGATTTCTTCTGCTTTGACGCGAGTTGATGTTTCGCATAAGGTTGAT
GATTCAAGTGGGTCAATTGGTCGCCGTTATGCACGTACTGATGAAATTGCAATTGCTTAT
GGCATCACAATCGATTTTGATACTGTCAAAGACAAAACTGTAACACTTCGTGAAAGAGAC
TCAATGACACAAATTAGAATCCCGATAGATGAAGTTGCAGAAGTTGTGAGAAATCTTTCA
TACAGTAAAATCGAATGGTCTGACGTTACCTCAAAATATCCCAAGTTTGAACAACAAGAA
AATGCAGCACAAAAGTAA

>g5191.t1 Gene=g5191 Length=745
MTVIVNLVRRIVNCSEIILKLNQNQVKQCARDFSITRKYFKNNQLANWGTKKAHRNIKLQ
LQLIQEMADPKIEEILAPLRAAVKEQGDLVRQLKSDGAPEIDVKKAIVELKARKKILEDK
ELSLAPQVASFDRAKMEDLLKRRFFYDQSFAIYGGITGQYDFGPMGCMLKANMLNLWRQF
FVLEEQMLEVDCSILTPEPVLKTSGHVDRFADLMVKDSKTGECFRLDHLIKAHLEKLASD
KKATQELKDECADIVVKLDGMNKQEMGDILKKFNMKSPLTQNELTEPIEFNLMFGTSIGP
TGLVKGFLRPETAQGIFVNFKRLLEFNQGRLPFAAAQIGNSFRNEISPRSGLIRVREFTM
AEIEHFCDPNLKDHPKFVDVADYEMTLYSACNQMDGNSASRITIGEAVKTGLVANETLGY
FMARIQMFLIKVGILPERLRFRQHMNNEMAHYACDCWDAECLTSYGWIECVGCADRSAYD
LTQHTNATGVRLTAEKKLPEPKTIEFTEAVPNMKILGKLFKKDAKEITELLSKLSIDDLK
KMNDELTQNNSYTLKSDANSYTLNNEMVTIKSGSKTIHVEEIIPSVIEPSFGIGRIMYAL
LEHRFQMRDGDEQRCFFSLPPIVAPLKCSVLPLSNNQEFTPFIKQISSALTRVDVSHKVD
DSSGSIGRRYARTDEIAIAYGITIDFDTVKDKTVTLRERDSMTQIRIPIDEVAEVVRNLS
YSKIEWSDVTSKYPKFEQQENAAQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5191.t1 CDD cd00935 GlyRS_RNA 76 126 8.22644E-25
24 g5191.t1 CDD cd00774 GlyRS-like_core 136 482 2.25759E-124
22 g5191.t1 CDD cd00858 GlyRS_anticodon 600 721 5.5955E-59
21 g5191.t1 Coils Coil Coil 736 745 -
17 g5191.t1 Gene3D G3DSA:1.10.287.10 - 65 137 7.2E-7
18 g5191.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 139 612 1.2E-220
20 g5191.t1 Gene3D G3DSA:1.20.1430.20 - 210 293 1.2E-220
19 g5191.t1 Gene3D G3DSA:1.10.30.30 - 498 575 1.2E-220
16 g5191.t1 Gene3D G3DSA:3.40.50.800 - 625 740 7.9E-43
4 g5191.t1 PANTHER PTHR10745:SF0 GLYCINE–TRNA LIGASE 130 735 2.5E-288
5 g5191.t1 PANTHER PTHR10745 GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2 130 735 2.5E-288
12 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 152 166 2.0E-55
7 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 288 300 2.0E-55
11 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 307 324 2.0E-55
9 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 339 356 2.0E-55
6 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 356 366 2.0E-55
10 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 584 596 2.0E-55
8 g5191.t1 PRINTS PR01043 Glycyl-tRNA synthetase signature 666 685 2.0E-55
2 g5191.t1 Pfam PF00458 WHEP-TRS domain 79 126 6.1E-10
1 g5191.t1 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 308 373 1.2E-9
3 g5191.t1 Pfam PF03129 Anticodon binding domain 627 718 2.3E-23
26 g5191.t1 ProSitePatterns PS00762 WHEP-TRS domain signature. 86 114 -
28 g5191.t1 ProSiteProfiles PS51185 WHEP-TRS domain profile. 75 131 12.269
29 g5191.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 264 625 10.33
25 g5191.t1 SMART SM00991 WHEP_TRS_a_2_a_3_a 79 134 7.1E-10
15 g5191.t1 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 78 118 2.86E-5
13 g5191.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 133 630 5.29E-124
14 g5191.t1 SUPERFAMILY SSF52954 Class II aaRS ABD-related 614 736 1.3E-34
27 g5191.t1 TIGRFAM TIGR00389 glyS_dimeric: glycine–tRNA ligase 133 718 2.9E-220

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5191/g5191.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5191.t1.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