Gene loci information

Transcript annotation

  • This transcript has been annotated as Bifunctional glutamate/proline–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_3 g3833 g3833.t6 TSS g3833.t6 28287301 28287301
chr_3 g3833 g3833.t6 isoform g3833.t6 28287380 28289943
chr_3 g3833 g3833.t6 exon g3833.t6.exon1 28287380 28288203
chr_3 g3833 g3833.t6 cds g3833.t6.CDS1 28287503 28288203
chr_3 g3833 g3833.t6 exon g3833.t6.exon2 28288260 28288522
chr_3 g3833 g3833.t6 cds g3833.t6.CDS2 28288260 28288522
chr_3 g3833 g3833.t6 exon g3833.t6.exon3 28288671 28289943
chr_3 g3833 g3833.t6 cds g3833.t6.CDS3 28288671 28289941
chr_3 g3833 g3833.t6 TTS g3833.t6 NA NA

Sequences

>g3833.t6 Gene=g3833 Length=2360
ATGCCAATTAAAGTAAATAGTGATTTAAAGAATCCACCAACCGGTAAGATATAGATTGAA
TAAAAAGTTACTTATGTATAAAGCTTAAAATTAATTATTTTCAATTTTTATGAAATATTT
TAAATGTTTTGTGAAATAAAATTTACAGATGGTGTGGATACCGCTGAAAATTTTTCATCT
CTTCCAAAAGACGCTAACTCTACAAAATCAAATAAACAAGAATCTCCAACAGCACTTGAT
GTTGACGATAGAAAGCAAGAAGGTAAATTTGTCGATCTTCCAGGAGCTGAAATGGGCAAA
GTTATTGTTCGCTTTCCTCCTGAAGCATCAGGATATTTGCACATTGGTCATGCTAAAGCA
GCTCTTTTAAATCAATATTATCAACAAGCATTTAATGGAAAACTGATTATGAGATTTGAC
GACACTAATCCAGCTAAAGAAAATGTTCACTTTGAAAACGTTATTTTAGAGGATTTAGAA
ATGCTTCAAATTAAACCAGATTTATTCACTTATACATCAGATTATTTTGAGCTCATGTTA
AAGTATTGTGAACAATTAATGAAAGAGAGAAAAGCATATGCTGACGATACTGATCCTGAA
CTGATGAAGCAAGAACGTGAACAGAGAGTTGAGTCTAAAAACAGAAACAACTCAATCGAA
AAGAATTTTGAAATGTGGAATGAAATGTTAGCTGGCACAGAAAAAGGACAGAAATGTTGT
ATCCGAGCGAAAATCGACATGTCTTCTCCAAATGGATGCCTTCGTGATCCAACAATTTAT
CGTTGCAAAAATGAGCCACATCCACGTACTGGAACTAAATACAAAGTTTATCCAACTTAT
GATTTTGCATGTCCAATTGTTGATGCAATTGAAAATGTAACTCATACTCTTCGTACAATG
GAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCATTAAAACTTCGTAAA
CCATATATTTGGGAATATTCTCGTTTAAATATGACTAACACAGTATTATCAAAACGTAAA
TTAACTTGGTTTGTTGAAAACGGTCTTGTTGATGGTTGGGATGATCCTCGCTTTCCTACA
GTTCGAGGTATTTTACGTCGTGGTATGACTGTTGAAGGTTTAAAACAATTCATTATTGCA
CAAGGTTCTAGTAAAGCTGTTGTATTTATGGAATGGGATAAAATTTGGGCTTTCAACAAA
AAAGTCATCGATCCAATTGCACCTAGATACATTGCATTAGAAAACGACAATCGTATAATT
GTCAAAGTTAATAATGCAATATTACAAGCTCTTGAAGTTCCAAGACATCCCAAAAATAAT
GAAGTTGGCACAAAAACTATTTGGGTTGGCCCAGAAATTTATATTGACTATGCTGATGCT
GAATCCTTAAAAGAAGGTGAAAATGCAACATTTATAAATTGGGGTAATTTAAGAATCAAA
AAGATTCATAAAGAAAGTGAAAAAATTACTTCTATCGATGCTGAATTGAATTTGAGTGAT
ACCGATTTCAAAAAGACATTAAAACTGACATGGCTTTGTAAACAGGATCCTTCAGAATAT
CCAACAACTTATTGCGTTTATTTCGATCATATAATTAGCAAAGCTGTTCTTGGTAAAAAT
GAAGACTTTAAAGCATATATCGGACATGAGACTAGAAAAGAAACAAAAATGTTGGCTGAT
CCTGAATTGAAAAAATGTCAGAAAGGCGATATCATTCAACTACAACGGCGCGGATTTTTC
AAAGTTGATCAAGCTTATGCTCCAGCTAGCGAAATTTCAGGATCAGAACGTCCAATTGTA
TTGTACTTTATTCCTGATGGTCACAAAAAAGAAATACCCACATCTGGTCTTTCAAAGAAA
CCTTCATGCTCCGAAAAAAAACAAAAATCCAAAAAAGTTACAACCGAGTCAAAAGACGAG
AGCCCAAGATTGAAAAAACAAACTCGATTGGGTTTGGAAGCTAAGAAAGAAGAGAATTTA
GCTGATTGGTATTCTCAAGTAATTACAAAGGGCGAAATGATTGAATATTATGATGTATCT
GGATGTTATATTCTTCGTCCATGGGCATTTGCAATCTGGAAGAATATTAAAAAATTTTTC
GATGCCAAAATTACTGATATGGGAGTAAAAGAATGCTATTTTCCAATGTTTGTTTCAAAA
GCTGCTTTGGAAAAAGAAAAAGATCATATCGCTGATTTTGCACCCGAAGTTGCTTGGGTT
ACAAAATCAGGTGAATCAGATTTGGCTGAGCCAATTGCTGTACGTCCAACTTCAGAAACT
GTCATGTATCCGGCATATTCTAAATGGATCCAATCTTATCGCGATTTGCCAATTCGTTTG
AATCAATGGAACAATGTTGT

>g3833.t6 Gene=g3833 Length=745
MFCEIKFTDGVDTAENFSSLPKDANSTKSNKQESPTALDVDDRKQEGKFVDLPGAEMGKV
IVRFPPEASGYLHIGHAKAALLNQYYQQAFNGKLIMRFDDTNPAKENVHFENVILEDLEM
LQIKPDLFTYTSDYFELMLKYCEQLMKERKAYADDTDPELMKQEREQRVESKNRNNSIEK
NFEMWNEMLAGTEKGQKCCIRAKIDMSSPNGCLRDPTIYRCKNEPHPRTGTKYKVYPTYD
FACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDALKLRKPYIWEYSRLNMTNTVLSKRKL
TWFVENGLVDGWDDPRFPTVRGILRRGMTVEGLKQFIIAQGSSKAVVFMEWDKIWAFNKK
VIDPIAPRYIALENDNRIIVKVNNAILQALEVPRHPKNNEVGTKTIWVGPEIYIDYADAE
SLKEGENATFINWGNLRIKKIHKESEKITSIDAELNLSDTDFKKTLKLTWLCKQDPSEYP
TTYCVYFDHIISKAVLGKNEDFKAYIGHETRKETKMLADPELKKCQKGDIIQLQRRGFFK
VDQAYAPASEISGSERPIVLYFIPDGHKKEIPTSGLSKKPSCSEKKQKSKKVTTESKDES
PRLKKQTRLGLEAKKEENLADWYSQVITKGEMIEYYDVSGCYILRPWAFAIWKNIKKFFD
AKITDMGVKECYFPMFVSKAALEKEKDHIADFAPEVAWVTKSGESDLAEPIAVRPTSETV
MYPAYSKWIQSYRDLPIRLNQWNNV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g3833.t6 CDD cd00807 GlnRS_core 59 368 1.12408E-138
18 g3833.t6 Coils Coil Coil 161 181 -
14 g3833.t6 Gene3D G3DSA:3.40.50.620 HUPs 29 368 2.8E-129
17 g3833.t6 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 369 545 3.9E-22
16 g3833.t6 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 374 476 3.9E-22
15 g3833.t6 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 611 745 2.5E-54
5 g3833.t6 Hamap MF_02076 Glutamate–tRNA ligase [gltX]. 2 563 30.672386
23 g3833.t6 MobiDBLite mobidb-lite consensus disorder prediction 18 34 -
24 g3833.t6 MobiDBLite mobidb-lite consensus disorder prediction 18 43 -
22 g3833.t6 MobiDBLite mobidb-lite consensus disorder prediction 572 608 -
21 g3833.t6 MobiDBLite mobidb-lite consensus disorder prediction 581 608 -
4 g3833.t6 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 29 596 0.0
3 g3833.t6 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 579 745 0.0
7 g3833.t6 PRINTS PR00987 Glutamyl-tRNA synthetase signature 63 75 9.1E-17
6 g3833.t6 PRINTS PR00987 Glutamyl-tRNA synthetase signature 77 88 9.1E-17
9 g3833.t6 PRINTS PR00987 Glutamyl-tRNA synthetase signature 92 105 9.1E-17
8 g3833.t6 PRINTS PR00987 Glutamyl-tRNA synthetase signature 237 247 9.1E-17
10 g3833.t6 PRINTS PR00987 Glutamyl-tRNA synthetase signature 253 261 9.1E-17
1 g3833.t6 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 59 363 3.8E-117
2 g3833.t6 Pfam PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain 366 542 7.4E-32
20 g3833.t6 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 66 77 -
26 g3833.t6 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 651 745 8.922
12 g3833.t6 SUPERFAMILY SSF52374 Nucleotidylyl transferase 59 371 6.97E-85
13 g3833.t6 SUPERFAMILY SSF50715 Ribosomal protein L25-like 366 568 3.82E-43
11 g3833.t6 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 617 745 2.27E-33
25 g3833.t6 TIGRFAM TIGR00463 gltX_arch: glutamate–tRNA ligase 31 545 5.1E-149

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:0005524 ATP binding MF
GO:0005737 cytoplasm CC
GO:0004818 glutamate-tRNA ligase activity MF
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0043039 tRNA aminoacylation BP
GO:0006412 translation BP
GO:0006424 glutamyl-tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF

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