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.t6 TTS g5191.t6 7587382 7587382
chr_2 g5191 g5191.t6 isoform g5191.t6 7587510 7589913
chr_2 g5191 g5191.t6 exon g5191.t6.exon1 7587510 7587808
chr_2 g5191 g5191.t6 exon g5191.t6.exon2 7587862 7588607
chr_2 g5191 g5191.t6 cds g5191.t6.CDS1 7588557 7588607
chr_2 g5191 g5191.t6 exon g5191.t6.exon3 7588664 7589542
chr_2 g5191 g5191.t6 cds g5191.t6.CDS2 7588664 7589542
chr_2 g5191 g5191.t6 exon g5191.t6.exon4 7589656 7589913
chr_2 g5191 g5191.t6 cds g5191.t6.CDS3 7589656 7589913
chr_2 g5191 g5191.t6 TSS g5191.t6 7590003 7590003

Sequences

>g5191.t6 Gene=g5191 Length=2182
ATGACAGTAATTGTAAATCTCGTTAGACGTATAGTGAATTGTAGTGAAATCATCCTCAAA
CTCAATCAAAATCAAGTGAAACAGTGCGCACGAGATTTTTCAATCACAAGGAAATATTTT
AAAAACAATCAATTAGCTAATTGGGGTACCAAAAAGGCTCATCGTAATATAAAATTACAA
TTGCAATTGATACAAGAGATGGCCGATCCAAAAATTGAAGAGATACTTGCTCCATTAAGA
GCTGCTGTGAAAGAGCAAGGTGATTTGGTTCGACAACTAAAGAGCGATGGAGCACCTGAA
ATCGATGTTAAAAAAGCAATTGTTGAGTTGAAGGCTCGTAAAAAGATTCTTGAGGATAAA
GAATTAAGTTTGGCACCACAAGTTGCTTCATTTGATCGTGCAAAAATGGAAGATTTATTG
AAAAGACGATTCTTTTATGACCAAAGTTTTGCGATTTATGGAGGAATCACAGGTCAATAT
GATTTTGGTCCAATGGGATGCATGTTGAAAGCAAATATGCTTAATTTATGGCGTCAATTC
TTTGTACTCGAGGAACAAATGCTTGAAGTTGACTGCTCAATTCTTACACCTGAGCCTGTT
CTTAAAACAAGCGGACATGTTGATCGTTTTGCTGATTTGATGGTGAAAGATTCAAAGACT
GGTGAATGTTTCAGATTGGATCATTTGATTAAGGCACATTTAGAAAAGCTAGCATCTGAT
AAGAAAGCAACACAAGAATTGAAAGATGAATGTGCTGATATTGTGGTCAAATTGGATGGA
ATGAATAAACAAGAGATGGGAGATATTCTCAAAAAATTTAACATGAAATCTCCATTGACT
CAAAATGAGCTCACTGAGCCTATTGAATTCAATTTGATGTTTGGAACAAGCATCGGACCA
ACTGGTTTAGTTAAAGGATTTTTGAGACCAGAAACGGCTCAAGGAATTTTCGTAAACTTC
AAACGATTACTTGAATTTAATCAAGGAAGATTGCCTTTTGCAGCAGCTCAAATCGGAAAT
TCTTTTCGTAATGAAATTTCTCCACGTTCAGGATTGATTCGTGTGCGTGAATTTACAATG
GCTGAAATTGAACATTTTTGTGATCCCAATTTAAAGGATCATCCAAAATTCGTTGATTGC
ATCTCGAATTACAATTGGAGAGGCTGTCAAAACTGGCTTGGTTGCTAATGAAACACTTGG
TTATTTTATGGCACGCATTCAAATGTTCCTTATTAAAGTTGGTATTTTACCAGAACGTCT
TCGTTTTAGACAACATATGAATAATGAAATGGCACATTATGCGTGTGATTGTTGGGATGC
AGAATGTTTGACAAGTTATGGATGGATCGAATGTGTTGGTTGTGCTGATCGTTCTGCTTA
TGATTTAACTCAGCATACAAATGCAACAGGTGTCAGGCTTACTGCTGAGAAAAAGTTACC
AGAGCCTAAAACTATTGAATTCACAGAAGCAGTTCCTAATATGAAAATTTTAGGAAAATT
ATTCAAGAAAGACGCAAAGGAGATTACAGAACTTCTTTCAAAATTATCAATTGATGATCT
TAAAAAAATGAATGATGAGCTTACACAAAATAATTCTTACACATTGAAATCAGATGCAAA
CTCATATACTCTTAATAATGAGATGGTAACCATCAAATCTGGATCTAAGACAATTCATGT
TGAGGAAATTATTCCATCAGTTATTGAACCGTCATTTGGAATTGGAAGAATTATGTATGC
GCTTTTGGAGCATCGTTTCCAAATGAGAGATGGAGATGAGCAACGTTGTTTCTTCTCACT
TCCACCTATTGTTGCACCTCTTAAATGCTCTGTTTTGCCGCTCAGTAATAATCAAGAATT
TACACCATTCATCAAACAGATTTCTTCTGCTTTGACGCGAGTTGATGTTTCGCATAAGGT
TGATGATTCAAGTGGGTCAATTGGTCGCCGTTATGCACGTACTGATGAAATTGCAATTGC
TTATGGCATCACAATCGATTTTGATACTGTCAAAGACAAAACTGTAACACTTCGTGAAAG
AGACTCAATGACACAAATTAGAATCCCGATAGATGAAGTTGCAGAAGTTGTGAGAAATCT
TTCATACAGTAAAATCGAATGGTCTGACGTTACCTCAAAATATCCCAAGTTTGAACAACA
AGAAAATGCAGCACAAAAGTAA

>g5191.t6 Gene=g5191 Length=395
MTVIVNLVRRIVNCSEIILKLNQNQVKQCARDFSITRKYFKNNQLANWGTKKAHRNIKLQ
LQLIQEMADPKIEEILAPLRAAVKEQGDLVRQLKSDGAPEIDVKKAIVELKARKKILEDK
ELSLAPQVASFDRAKMEDLLKRRFFYDQSFAIYGGITGQYDFGPMGCMLKANMLNLWRQF
FVLEEQMLEVDCSILTPEPVLKTSGHVDRFADLMVKDSKTGECFRLDHLIKAHLEKLASD
KKATQELKDECADIVVKLDGMNKQEMGDILKKFNMKSPLTQNELTEPIEFNLMFGTSIGP
TGLVKGFLRPETAQGIFVNFKRLLEFNQGRLPFAAAQIGNSFRNEISPRSGLIRVREFTM
AEIEHFCDPNLKDHPKFVDCISNYNWRGCQNWLGC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5191.t6 CDD cd00935 GlyRS_RNA 76 126 5.29696E-25
12 g5191.t6 Gene3D G3DSA:1.10.287.10 - 65 133 3.0E-7
13 g5191.t6 Gene3D G3DSA:1.20.1430.20 - 209 292 8.6E-32
3 g5191.t6 PANTHER PTHR10745:SF0 GLYCINE–TRNA LIGASE 130 380 1.3E-127
4 g5191.t6 PANTHER PTHR10745 GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2 130 380 1.3E-127
9 g5191.t6 PRINTS PR01043 Glycyl-tRNA synthetase signature 152 166 6.2E-39
6 g5191.t6 PRINTS PR01043 Glycyl-tRNA synthetase signature 288 300 6.2E-39
8 g5191.t6 PRINTS PR01043 Glycyl-tRNA synthetase signature 307 324 6.2E-39
7 g5191.t6 PRINTS PR01043 Glycyl-tRNA synthetase signature 339 356 6.2E-39
5 g5191.t6 PRINTS PR01043 Glycyl-tRNA synthetase signature 356 366 6.2E-39
2 g5191.t6 Pfam PF00458 WHEP-TRS domain 79 126 2.7E-10
1 g5191.t6 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 308 373 8.5E-10
15 g5191.t6 ProSitePatterns PS00762 WHEP-TRS domain signature. 86 114 -
18 g5191.t6 ProSiteProfiles PS51185 WHEP-TRS domain profile. 75 131 12.269
19 g5191.t6 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 264 366 8.817
16 g5191.t6 SMART SM00991 WHEP_TRS_a_2_a_3_a 79 134 7.1E-10
11 g5191.t6 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 78 118 1.22E-5
10 g5191.t6 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 133 372 2.11E-86
17 g5191.t6 TIGRFAM TIGR00389 glyS_dimeric: glycine–tRNA ligase 133 379 5.9E-96

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5191/g5191.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5191.t6.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