Gene loci information

Transcript annotation

  • This transcript has been annotated as Histidine–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_1 g14000 g14000.t5 TTS g14000.t5 33944837 33944837
chr_1 g14000 g14000.t5 isoform g14000.t5 33944910 33946974
chr_1 g14000 g14000.t5 exon g14000.t5.exon1 33944910 33946355
chr_1 g14000 g14000.t5 cds g14000.t5.CDS1 33944910 33946355
chr_1 g14000 g14000.t5 exon g14000.t5.exon2 33946425 33946602
chr_1 g14000 g14000.t5 cds g14000.t5.CDS2 33946425 33946565
chr_1 g14000 g14000.t5 exon g14000.t5.exon3 33946882 33946974
chr_1 g14000 g14000.t5 TSS g14000.t5 33947054 33947054

Sequences

>g14000.t5 Gene=g14000 Length=1717
ATGAGTGAAAACCGAGAAGAAATTCAGGAACAAATAAAGGTTCAAGGTGATCTTGTGCGT
AAACTTAAAGCTGCCAAGGAATCGAAAGAAAAGTAATCCAGTAATAAAAGCTGTACGTGT
TGTTGTCGAGATGTTGAAAAATTTTATGCAATTATTATTTAGAAATTCAAAAAGAAATCA
ATTACTTCACGTTTGTCGCTTTTGCTCCTCGACTTCTGGCGTATCGCTTCAGGACAAAAG
AATAAACGAAATTAGAAAAAATATTTTGCAGATTGATGAAGAAGTTGCAAAGTTATTAGC
ATTGAAGGCAAAGCTAAATGAAAATGAACCAGCAGCGCCTTTAAAATTCACTCTTAAAAC
GCCTAAAGGCACACGAGATTATGCTCCTGAGCAAATGACTCTTCGACAAAGTGTTTTGAA
CACAATAGTATCTGTTTTTAAAAAGCACGGTGCTGACACTATAGATACACCGGTTTTTGA
ATTAAAAGAAGTTTTAACTGGAAAATATGGTGAAGATTCTAAACTCATTTATGATCTTAA
AGATCAAGGAGGAGAAATTTTGTCAATGCGTTATGATTTGACAGTACCTCTTGCTCGTTA
TTTAGCAATGAATAAAGTATCAAATATCAAGAGATATCACATAGCAAAAGTTTACCGTCG
TGACAATCCAGCAATGACAAAAGGAAGGTATCGCGAGTTTTACCAATGTGATTTTGATAT
TGCTGGAACTTATGATCCTATGCTTCCTGATGCCGAATGTGTAAAAGTTGTCTCTGAAAT
TTTATCATCTTTAGACATTGGTGCATTTGTTATTAAATTGAATCATCGTAAACTTCTTGA
TGGAATGTTTGAAGCATGTGGCGTTCCGGCAGAGAAATTTCGCACAATTTGTTCAGCTGT
TGATAAGTTGGATAAATCACCATGGGAAGATGTCAAAAAAGAAATGATTGATGAGAAAGG
TTTAGATGATGCAACCGCTAATAAGATTGGTGAATATGTTCGATTGAATGGTGGTGAAGA
ACTTGTCGATAAATTATTAACTGATGAAAAATTGAAGAAGGTGAAGTCAGCAGTTGCGGG
ATTGGAAGACATGAAACTGTTGCTAAAATACTGTAAAATTTTCAATGTTATGCATCAAGT
GCGTTTCGATTTGAGTCTTGCTAGAGGTCTCGACTATTATACTGGTGTTATTTATGAAGC
TGTTCTTTTAAATCAAGAAAAGAAACGTAAAAAGGATGAAGAGACAGAAATTGGATCAGT
CGCTGGTGGAGGACGTTATGATAATCTTGTTGGTATGTTCGATTCAAAAGGCAAACAAGT
TCCTTGTGTTGGTGTTTCTATTGGTGTTGAAAGAGTTTTTGCAATTATTGAAGCGAAGAA
TGCAGCAAACAAGACGAAAATAAGAACGAGTGAGATTCAAATCTTTGTAGCATCAGCACA
TAAGGGATTGCATGAAAAGCGTTTAGAAATTCTTTCTAAATTATGGGATGGAGGCATAAA
AGCAGAACATTCCTATAAATCAAATCCAAAATTGCTAGCTCAGCTGCAATATTGTGAAGA
GCAGCAAATTCCTTTTGCATTGGTGCTCGGTGACAGTGAATTAGAACGTGGAGTTATAAA
ATTACGTGATGTTGTAACACGTAAAGAAGAAGAAATTCCATTGGATAATTTGGTTGAAGC
AATTAAATGGCGTTTGAGTAATAAAGGTTATAACTAA

>g14000.t5 Gene=g14000 Length=528
MLKNFMQLLFRNSKRNQLLHVCRFCSSTSGVSLQDKRINEIRKNILQIDEEVAKLLALKA
KLNENEPAAPLKFTLKTPKGTRDYAPEQMTLRQSVLNTIVSVFKKHGADTIDTPVFELKE
VLTGKYGEDSKLIYDLKDQGGEILSMRYDLTVPLARYLAMNKVSNIKRYHIAKVYRRDNP
AMTKGRYREFYQCDFDIAGTYDPMLPDAECVKVVSEILSSLDIGAFVIKLNHRKLLDGMF
EACGVPAEKFRTICSAVDKLDKSPWEDVKKEMIDEKGLDDATANKIGEYVRLNGGEELVD
KLLTDEKLKKVKSAVAGLEDMKLLLKYCKIFNVMHQVRFDLSLARGLDYYTGVIYEAVLL
NQEKKRKKDEETEIGSVAGGGRYDNLVGMFDSKGKQVPCVGVSIGVERVFAIIEAKNAAN
KTKIRTSEIQIFVASAHKGLHEKRLEILSKLWDGGIKAEHSYKSNPKLLAQLQYCEEQQI
PFALVLGDSELERGVIKLRDVVTRKEEEIPLDNLVEAIKWRLSNKGYN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g14000.t5 CDD cd00773 HisRS-like_core 88 414 1.00865E-105
17 g14000.t5 CDD cd00859 HisRS_anticodon 428 519 2.34091E-26
10 g14000.t5 Coils Coil Coil 38 65 -
9 g14000.t5 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 64 424 1.3E-161
8 g14000.t5 Gene3D G3DSA:3.40.50.800 - 425 525 3.4E-29
5 g14000.t5 Hamap MF_00127 Histidine–tRNA ligase [hisS]. 73 520 23.832239
3 g14000.t5 PANTHER PTHR11476 HISTIDYL-TRNA SYNTHETASE 32 523 6.5E-221
4 g14000.t5 PANTHER PTHR11476:SF8 HISTIDINE–TRNA LIGASE, CYTOPLASMIC 32 523 6.5E-221
16 g14000.t5 PIRSF PIRSF001549 His-tRNA_synth 71 522 4.7E-126
1 g14000.t5 Pfam PF13393 Histidyl-tRNA synthetase 80 409 2.8E-44
2 g14000.t5 Pfam PF03129 Anticodon binding domain 430 519 3.0E-15
12 g14000.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 30 -
13 g14000.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 17 -
14 g14000.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 18 25 -
15 g14000.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 26 30 -
11 g14000.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 31 528 -
20 g14000.t5 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 49 413 11.634
6 g14000.t5 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 75 414 4.78E-80
7 g14000.t5 SUPERFAMILY SSF52954 Class II aaRS ABD-related 427 521 4.58E-20
19 g14000.t5 TIGRFAM TIGR00442 hisS: histidine–tRNA ligase 76 510 4.5E-98

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:0004821 histidine-tRNA ligase activity MF
GO:0006427 histidyl-tRNA aminoacylation BP
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