Gene loci information

Transcript annotation

  • This transcript has been annotated as Cysteine–tRNA ligase, cytoplasmic.

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 g1919 g1919.t1 TSS g1919.t1 13861421 13861421
chr_3 g1919 g1919.t1 isoform g1919.t1 13861473 13863709
chr_3 g1919 g1919.t1 exon g1919.t1.exon1 13861473 13861605
chr_3 g1919 g1919.t1 cds g1919.t1.CDS1 13861473 13861605
chr_3 g1919 g1919.t1 exon g1919.t1.exon2 13861662 13863709
chr_3 g1919 g1919.t1 cds g1919.t1.CDS2 13861662 13863709
chr_3 g1919 g1919.t1 TTS g1919.t1 NA NA

Sequences

>g1919.t1 Gene=g1919 Length=2181
ATGTCTAGAAAACAACAAGATTGGATTGCACCAAACGATACAGCTCCAAAGCTAAAACTT
TTTAATAGTCTAACAAGAAAAAAGGAAGTATTTGTGCCTCAAGATGGAAAAATTGTAAAA
TGGTATTCTTGCGGTCCTACCGTTTATGATGCATCACATATGGGTCATGCTCGTTCATAT
ATCTCATTTGATATTCTTAGACGAGTTCTTGCCGATTATTTTGGCTATCAAATTCATTTT
GTAATGAACATTACCGATATTGATGACAAAATTATCAAAAGAGCGAGACAAAACTTTCTG
TTTGAAGAATATTTGAAGAAAAATGTCTCACTTGAAGATTTTATTGCTGATGTCAACACG
TCAATGGAAATATTTCGTAAGAAAAAGGCAGAAAATAAAGATCCAGATAAAGCAATAATG
ATGGACCGCATTGTAATGAGTGTAGAAGAAGCTGAAAATAATTTACGTAAAGCTGTTGAA
ACAGCAAATGATGAAGATATTAACAAATCGAGAGTACAGTTGCAAGAAGCTGCAAAATCG
CCCATTTGTGATTGGCTTGATAATCAATATGGTGCAACTGTAAGAGATAAGAAAATATTT
GAAAATTTAACTAGATTTTGGGAAAATGAATATAACAATGATATGAATGCACTAAATGTA
TTACCGCCTCATGTTCTCACACGCGTAACAGAATATGTTCCTGAGATTATCACTTTTATT
GAAAAGATTATTGTAAATGGTTATGGATATGAGTCTAATGGTTCCGTATATTTTGATGTT
GCTAAATTTGATGCAGCTAAACAACATCATTATGCTAAACTTGTGCCAGAGGCTTTTGGA
GATACTGCTCAATTGCAAGAAGGCGAAGGTGATTTGAGTGGTGATAAAGGTCAGGAAAAA
CGGTCACCTAATGATTTTGCGTTATGGAAGAATAGTAAAGAAGGTGAACCTGCTTGGAAT
TCGCCTTGGGGTCAAGGAAGACCAGGCTGGCACATTGAATGTTCCGCGATGGCTTCTGAA
ATATTCAAAGGTGATCTTGACATTCATACAGGTGGTGTCGATTTAAAATTTCCACATCAT
GATAATGAAATTGCACAGAGCGAAGCTCATTTTGATACTAGTGGATGGGTTAAATATTTT
CTTCATACTGGACATTTAACAATTAGTGGTTGCAAAATGTCAAAATCATTGAAAAATTTC
ATCACAATTAAGGAAGCTCTGAAGCAACATACAGCTACACAAATACGATTTGCATTCTTA
TTGCATTCATGGAAAGATACACTTGATTATAGTGCAAATACAATGGAAATTGCTATTAGA
TATGAAAAAATGCTTAATGAGTTCTTCCTCAATGTAAAGGATTTTATTCGTCAACGAAAG
AGCAATGAAATGGTTAAGTTTACAGAACGCGATCTTGAATTGAGTCGGAAGTTTTATGAT
ACTAAAAGAGCTGTGCATGAAGCATTGTGTGACAATATTGATACAAAATCAGCACTTGAT
GCCATTCGTGAACTCATTTCATATGCAAATATTTATATTCGTGACATGCAAGCTAATGTA
AATGTTCAATTACTCGAAGACATTGCAGTTTACATCACAGACTTGCTTGAGATATTTGGG
GCAATTTCTCGTAGTAGTAATAAAAAATCCATCGGTTTTCCATCTATCTCTGGTGATTCA
AATGGAACTAATAAGGAAGAGATTTTATTGCCTTATTTATCAGCTTTAGCTGATTTTAGA
AAAGTCGTTCGTGAAAATGCACTTGAAGTAAAAGCGGTTAAAATTCTTCAATTATGTGAT
GAGTTACGGGATGAAATTTTACCAAATTTGAGTGTTCGATTAGAAGATAAAGAAGGTCAA
TCAGTAATTAAACTCGTTGATCGTGAAGTTCTTATGAAAGAGAAAGAAGAGAAGAAACGA
CGTGAAGAGCAGAAAAAAGCAGAGCAATTAGCAAAAGCAGAATTACAACGCCAAAAAGAG
AAAGAACGTGAGGAGCAAAGAAAAATTAATCCAAAAGATATGTTTAGAAATCAAACTGAC
AAGTACTCAGCATTCGATGATGAAGGTTTACCAACACTTGATCATGAAGGTAAAGAAATT
AGCAAAGGTCAACAGAAGAAATTGAAAAAGTTACAACAGCAACAAGAAGTCAAGTATGCC
GAATATCTCAAATCAATTTAA

>g1919.t1 Gene=g1919 Length=726
MSRKQQDWIAPNDTAPKLKLFNSLTRKKEVFVPQDGKIVKWYSCGPTVYDASHMGHARSY
ISFDILRRVLADYFGYQIHFVMNITDIDDKIIKRARQNFLFEEYLKKNVSLEDFIADVNT
SMEIFRKKKAENKDPDKAIMMDRIVMSVEEAENNLRKAVETANDEDINKSRVQLQEAAKS
PICDWLDNQYGATVRDKKIFENLTRFWENEYNNDMNALNVLPPHVLTRVTEYVPEIITFI
EKIIVNGYGYESNGSVYFDVAKFDAAKQHHYAKLVPEAFGDTAQLQEGEGDLSGDKGQEK
RSPNDFALWKNSKEGEPAWNSPWGQGRPGWHIECSAMASEIFKGDLDIHTGGVDLKFPHH
DNEIAQSEAHFDTSGWVKYFLHTGHLTISGCKMSKSLKNFITIKEALKQHTATQIRFAFL
LHSWKDTLDYSANTMEIAIRYEKMLNEFFLNVKDFIRQRKSNEMVKFTERDLELSRKFYD
TKRAVHEALCDNIDTKSALDAIRELISYANIYIRDMQANVNVQLLEDIAVYITDLLEIFG
AISRSSNKKSIGFPSISGDSNGTNKEEILLPYLSALADFRKVVRENALEVKAVKILQLCD
ELRDEILPNLSVRLEDKEGQSVIKLVDREVLMKEKEEKKRREEQKKAEQLAKAELQRQKE
KEREEQRKINPKDMFRNQTDKYSAFDDEGLPTLDHEGKEISKGQQKKLKKLQQQQEVKYA
EYLKSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1919.t1 CDD cd00672 CysRS_core 19 431 3.45321E-101
12 g1919.t1 Coils Coil Coil 141 168 -
11 g1919.t1 Coils Coil Coil 625 668 -
4 g1919.t1 Hamap MF_00041 Cysteine–tRNA ligase [cysS]. 18 625 29.70483
14 g1919.t1 MobiDBLite mobidb-lite consensus disorder prediction 635 711 -
2 g1919.t1 PANTHER PTHR10890:SF3 CYSTEINE–TRNA LIGASE, CYTOPLASMIC 14 716 1.3E-246
3 g1919.t1 PANTHER PTHR10890 CYSTEINYL-TRNA SYNTHETASE 14 716 1.3E-246
7 g1919.t1 PRINTS PR00983 Cysteinyl-tRNA synthetase signature 41 52 9.5E-29
8 g1919.t1 PRINTS PR00983 Cysteinyl-tRNA synthetase signature 78 87 9.5E-29
6 g1919.t1 PRINTS PR00983 Cysteinyl-tRNA synthetase signature 316 334 9.5E-29
5 g1919.t1 PRINTS PR00983 Cysteinyl-tRNA synthetase signature 347 368 9.5E-29
1 g1919.t1 Pfam PF01406 tRNA synthetases class I (C) catalytic domain 32 438 1.9E-124
9 g1919.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 18 436 4.35E-83
10 g1919.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 472 621 7.85E-11
15 g1919.t1 TIGRFAM TIGR00435 cysS: cysteine–tRNA ligase 18 624 1.6E-145

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:0004817 cysteine-tRNA ligase activity MF
GO:0006423 cysteinyl-tRNA aminoacylation BP
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
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