Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable glutamate–tRNA ligase, mitochondrial.

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_1 g11138 g11138.t1 TSS g11138.t1 14305855 14305855
chr_1 g11138 g11138.t1 isoform g11138.t1 14305870 14309496
chr_1 g11138 g11138.t1 exon g11138.t1.exon1 14305870 14306294
chr_1 g11138 g11138.t1 cds g11138.t1.CDS1 14305870 14306294
chr_1 g11138 g11138.t1 exon g11138.t1.exon2 14306349 14307641
chr_1 g11138 g11138.t1 cds g11138.t1.CDS2 14306349 14307641
chr_1 g11138 g11138.t1 exon g11138.t1.exon3 14307844 14307941
chr_1 g11138 g11138.t1 cds g11138.t1.CDS3 14307844 14307941
chr_1 g11138 g11138.t1 exon g11138.t1.exon4 14308006 14309199
chr_1 g11138 g11138.t1 cds g11138.t1.CDS4 14308006 14309199
chr_1 g11138 g11138.t1 exon g11138.t1.exon5 14309261 14309496
chr_1 g11138 g11138.t1 cds g11138.t1.CDS5 14309261 14309496
chr_1 g11138 g11138.t1 TTS g11138.t1 14309565 14309565

Sequences

>g11138.t1 Gene=g11138 Length=3246
ATGATTTCGCGTGTGATTTTTTGTAAAAATAAAAATTTTCAATTAATACGATATTTATCA
ACTGCCTTGCAGCATGAAACAGCTACAACAACGGTGGAGTATCCACCTATCATTGACATG
TCTAAAGAGGCAAAAGAAATGAGGAAAAAACTAGAATGGCATGATAAAATTAAGCGGTCA
CCTACTATAGAAGAGAAAATTATTCAAATAAATATGCCTCGATTCTATGGATTTAAATGT
CTGATGCTTGATGGAACAAAATATCCTTACAATTCAAATGATTTTATCAAATATATAACC
AAGACAGAGTTCCAAGAATTAGCAAACAAAATCGATGAAAAAGAGTCGAAAAAAATTGAT
GGATTCTTAAATCTCATTAAATCTGATATTCAAGATGCAATTGAATTTGAAATTGATTCT
TGCAATCATTATTTCGATGATTCAATGCATCCAAGAGAGATACAGCGAGAAAAAGCAAGT
CGTTTAGTTAAACAGTTGAATAGAATTCTTATTTCTGCTCTTGGCGCTGACAACCATCAT
CTTTTCGAAGCAGACACTGATATTGATCCAAGAGTAGAAGCATTTTGGTTCGTTGGTCGT
TTTGTTCCGCCAAAGAGAGTTCAATTTTGGCGAAGTATGAAAGATCATCTTAAAGATTAT
AAAATGGATCCAGTAGATAGACCATTTCAATATGTAGGAAAACCGCTTCTTACATTAAGA
CATCAATATCCACTTGAGCCTTTTGACGAAATAGATTTCAGCTCATTAACAGCTTGTAAT
GAAAATATTCCTTTCGAATCTGTTTCATCAATAGATCCTGTATCTCATGGTTGGCATTTT
CATCATCGTCATGCTGTCTGTGTACCTGGTTTTTGGGCCGGAAATGTCCGTGAATATGGT
CTTTTATCTTATCACGATCGTGGATTTATGTATCATAGAACGAAAAAGAATTATGGAAAA
GAAGATGATCAAGAAGCAATTCATTCACATGGCATATTATCTTCATATGCATGGGCATAC
ACCCAAGCTTGTTATCAAGGTTTCTCGACTTATAATGACATGACTTATCCATTATCAACA
CAATCAATTGTCACTGATGGTCAAAATTGGTCATTTTATAGATATCAACTCAATACATCA
ATAATGCACACAGAAGTTGATGCTCCAAATTATAAATACAATCAGTGTTGGGGCACAAAT
GACATGAAATTGTATGAACACATTGATGAGAATGGTAAAATTCAAGGATTGAATGATGAT
GTGTTAAGACATTTAATTCAATTTTATATTAACGAACCAAAAATGAGAAATTATGAGATG
AAACCATATCTCGATCCGAAAGAAAAGAAAATAGCAGATATTGAAGATGTTGATAGAAGG
CAATGGTTAGAAAAGACATATAAATATCTTGTTGCTAATCGTCCAAGAACAAAGAATATG
GTACCAGAGATTTATCATTGGGAATACATTTATAAAATTCTATTTAAAACAATGCATATG
GATAATAAGACTCGCTTCTTTGAACTTGGCATTAATCCATATCTTAGACGTCTGGATGAG
CATATTCCAGAATATATTCCTCGTGATTTTAGACCAAATGGCATTCATGATAAGAAGAAG
AGACGTGCGACATATTATCCTCTAGATCATCGTTCAAATGATCCACGAACAATGAGTCAT
TCATTATTTGGTGCTGCAAAGGAAGGTGTGAGAAGAAACTATTTTAAAAGAATAATTAAT
GAAGACTTGTTTAAAATCAGCCGAAAATATAGTACTGATAAAGAAGTACGAGTGAGATTT
GCTCCATCACCAACTGGATTTTTACATCTTGGTGGATTAAGGACAGCATTGTTCAATTAT
CTTTTTGCAAAAGCTAATAATGGTAAATTCATTTTAAGAATAGAGGATACTGATCAAACA
AGACTTGTTGAGGGTGCAACAGAACAATTAATGAGAGATTTAGAATGGGCTGGTATGAGA
GCAGATGAGGGGCCGCTTGAATACGGAGGAAATTTTGGTCCATATATACAAAGTCAACGA
TTAGACATTTATCAAAAACACATTCAAACGCTACTTGAAAATGGTAGCGCATATCATTGT
TTTTGCAGTGAAAGAAGACTTGAATTATTGAGAAAAGAAGCTTTAAAAGCACGCCAAATT
CCTAAATATGACAACAGATGCAGACATCTCACTCCAGGACAAATTGCAGAAAAAATTGCA
AAGGGTGACAAATATTGTATAAGATTTAAATTACATGATACTGGTGAATCATTTATTGAT
TTAATCTATGGAAATTATGTCTACTATGTCGCACAAAATGAGGGCGATCCTGTTATTCTT
AAAAGTGATGGTTATCCTACTTATCATTTTGCAAATGTCGTTGATGACCATTTAATGGAA
ATAAGTCATGTGTTGAGAGGAGTAGAATGGCAGATATCTACACCAAAGCATTTAATGATG
TATAGAGCATTAGGATTTACACCACCTGTTTTCGGACATTTGCCACTTATAATGAATGCA
GATGGAAGCAAGTTAAGTAAGAGACAAAACGATATTAAACTTGAATTCTATAAAACGAGA
GGATATTTTCCACAAGCTTTGCTCAATTATATTACACAAGCTGGAGGAGGCTTTAATCGA
GATCCAAGCGAACGATTATACTGTTATGATATGAAACATTTAACAAAAAAGTTTGACATT
ACACGAATCAATTCAAATTCTAGTCGACTAAATCCAGAACTGTTAAATGACCTAAATCGT
CTCGAATTAATTAATCAAATTGAAAATCCTGAGCAATGCAAAGTCCTAATTGAAAATGTT
CGTACACTTATTAAAACAAAATATCCGTTAAATGCTGATCAATTGGACCTTGATGATGAT
CATATATTAAGTGTCTTAAAATGGGCATCAAAAAGAATTAGCACAATAAATGAACTAGCT
GAAGAAAATCTTTCTTTTCTTTGGGTTCTTCCTAAAATTACAAAGGACAAAGAGATTGAA
TTGAATGAAGCAATAATCGATTCATTAGTTGAAGAATTAAAAGACGAAAACTTTAATAAG
CAAAATCTTCAACAAATACTCAAAGAGTTTTCAAACGAGAAAAATCTGACGTTTGCCAAC
TTTATGAAAAATTTACGAACAATGTTGAGTGGCCTCAAAGAAGGACCGGGTGTAGCTGAA
ATGATGGAGATATTAGGCAAAGAAGATACACTTGAACGAATTATTCGATTAAAAAAGAAA
AAGTAA

>g11138.t1 Gene=g11138 Length=1081
MISRVIFCKNKNFQLIRYLSTALQHETATTTVEYPPIIDMSKEAKEMRKKLEWHDKIKRS
PTIEEKIIQINMPRFYGFKCLMLDGTKYPYNSNDFIKYITKTEFQELANKIDEKESKKID
GFLNLIKSDIQDAIEFEIDSCNHYFDDSMHPREIQREKASRLVKQLNRILISALGADNHH
LFEADTDIDPRVEAFWFVGRFVPPKRVQFWRSMKDHLKDYKMDPVDRPFQYVGKPLLTLR
HQYPLEPFDEIDFSSLTACNENIPFESVSSIDPVSHGWHFHHRHAVCVPGFWAGNVREYG
LLSYHDRGFMYHRTKKNYGKEDDQEAIHSHGILSSYAWAYTQACYQGFSTYNDMTYPLST
QSIVTDGQNWSFYRYQLNTSIMHTEVDAPNYKYNQCWGTNDMKLYEHIDENGKIQGLNDD
VLRHLIQFYINEPKMRNYEMKPYLDPKEKKIADIEDVDRRQWLEKTYKYLVANRPRTKNM
VPEIYHWEYIYKILFKTMHMDNKTRFFELGINPYLRRLDEHIPEYIPRDFRPNGIHDKKK
RRATYYPLDHRSNDPRTMSHSLFGAAKEGVRRNYFKRIINEDLFKISRKYSTDKEVRVRF
APSPTGFLHLGGLRTALFNYLFAKANNGKFILRIEDTDQTRLVEGATEQLMRDLEWAGMR
ADEGPLEYGGNFGPYIQSQRLDIYQKHIQTLLENGSAYHCFCSERRLELLRKEALKARQI
PKYDNRCRHLTPGQIAEKIAKGDKYCIRFKLHDTGESFIDLIYGNYVYYVAQNEGDPVIL
KSDGYPTYHFANVVDDHLMEISHVLRGVEWQISTPKHLMMYRALGFTPPVFGHLPLIMNA
DGSKLSKRQNDIKLEFYKTRGYFPQALLNYITQAGGGFNRDPSERLYCYDMKHLTKKFDI
TRINSNSSRLNPELLNDLNRLELINQIENPEQCKVLIENVRTLIKTKYPLNADQLDLDDD
HILSVLKWASKRISTINELAEENLSFLWVLPKITKDKEIELNEAIIDSLVEELKDENFNK
QNLQQILKEFSNEKNLTFANFMKNLRTMLSGLKEGPGVAEMMEILGKEDTLERIIRLKKK
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g11138.t1 CDD cd00808 GluRS_core 595 925 7.3563E-116
16 g11138.t1 Coils Coil Coil 1006 1033 -
15 g11138.t1 Coils Coil Coil 1067 1081 -
13 g11138.t1 Gene3D G3DSA:3.40.50.620 HUPs 586 925 1.9E-131
14 g11138.t1 Gene3D G3DSA:1.10.10.350 - 987 1081 1.6E-17
5 g11138.t1 Hamap MF_00022 Glutamate–tRNA ligase [gltX]. 595 1078 27.689318
3 g11138.t1 PANTHER PTHR43311:SF2 GLUTAMATE–TRNA LIGASE, MITOCHONDRIAL-RELATED 588 1076 7.6E-163
4 g11138.t1 PANTHER PTHR43311 GLUTAMATE–TRNA LIGASE 588 1076 7.6E-163
9 g11138.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 599 611 4.1E-25
8 g11138.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 613 624 4.1E-25
6 g11138.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 628 641 4.1E-25
7 g11138.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 786 796 4.1E-25
10 g11138.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 802 810 4.1E-25
2 g11138.t1 Pfam PF07147 Mitochondrial 28S ribosomal protein S30 (PDCD9) 12 433 1.1E-114
1 g11138.t1 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 595 915 2.8E-93
18 g11138.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 602 613 -
12 g11138.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 596 905 2.47E-102
11 g11138.t1 SUPERFAMILY SSF48163 An anticodon-binding domain of class I aminoacyl-tRNA synthetases 891 1074 9.42E-21
19 g11138.t1 TIGRFAM TIGR00464 gltX_bact: glutamate–tRNA ligase 595 1075 2.1E-131

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005840 ribosome CC
GO:0005524 ATP binding MF
GO:0000049 tRNA binding MF
GO:0004818 glutamate-tRNA ligase activity MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0043039 tRNA aminoacylation BP
GO:0008270 zinc ion binding MF
GO:0006424 glutamyl-tRNA aminoacylation BP
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005739 mitochondrion 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