General information for g14000.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histidine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g14000 is located on chr_1: 33944910..33946974 (- strand)
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.t2 | TTS | g14000.t2 | 33944837 | 33944837 |
| chr_1 | g14000 | g14000.t2 | isoform | g14000.t2 | 33944848 | 33945604 |
| chr_1 | g14000 | g14000.t2 | exon | g14000.t2.exon1 | 33944848 | 33945604 |
| chr_1 | g14000 | g14000.t2 | cds | g14000.t2.CDS1 | 33944910 | 33945536 |
| chr_1 | g14000 | g14000.t2 | TSS | g14000.t2 | NA | NA |
Sequences
>g14000.t2 Gene=g14000 Length=757
TTGTCGATAAATTATTAACTGATGAAAAATTGAAGAAGGTGAAGTCAGCAGTTGCGGGAT
TGGAAGACATGAAACTGTTGCTAAAATACTGTAAAATTTTCAATGTTATGCATCAAGTGC
GTTTCGATTTGAGTCTTGCTAGAGGTCTCGACTATTATACTGGTGTTATTTATGAAGCTG
TTCTTTTAAATCAAGAAAAGAAACGTAAAAAGGATGAAGAGACAGAAATTGGATCAGTCG
CTGGTGGAGGACGTTATGATAATCTTGTTGGTATGTTCGATTCAAAAGGCAAACAAGTTC
CTTGTGTTGGTGTTTCTATTGGTGTTGAAAGAGTTTTTGCAATTATTGAAGCGAAGAATG
CAGCAAACAAGACGAAAATAAGAACGAGTGAGATTCAAATCTTTGTAGCATCAGCACATA
AGGGATTGCATGAAAAGCGTTTAGAAATTCTTTCTAAATTATGGGATGGAGGCATAAAAG
CAGAACATTCCTATAAATCAAATCCAAAATTGCTAGCTCAGCTGCAATATTGTGAAGAGC
AGCAAATTCCTTTTGCATTGGTGCTCGGTGACAGTGAATTAGAACGTGGAGTTATAAAAT
TACGTGATGTTGTAACACGTAAAGAAGAAGAAATTCCATTGGATAATTTGGTTGAAGCAA
TTAAATGGCGTTTGAGTAATAAAGGTTATAACTAATTTATTGTGCACCATTTTTATGATT
TTATCATTGAACATTTTCTTTTTGATAATAAAATAGC
>g14000.t2 Gene=g14000 Length=208
MKLLLKYCKIFNVMHQVRFDLSLARGLDYYTGVIYEAVLLNQEKKRKKDEETEIGSVAGG
GRYDNLVGMFDSKGKQVPCVGVSIGVERVFAIIEAKNAANKTKIRTSEIQIFVASAHKGL
HEKRLEILSKLWDGGIKAEHSYKSNPKLLAQLQYCEEQQIPFALVLGDSELERGVIKLRD
VVTRKEEEIPLDNLVEAIKWRLSNKGYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g14000.t2 | CDD | cd00859 | HisRS_anticodon | 108 | 199 | 0 |
| 8 | g14000.t2 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 1 | 104 | 0 |
| 7 | g14000.t2 | Gene3D | G3DSA:3.40.50.800 | - | 105 | 205 | 0 |
| 3 | g14000.t2 | PANTHER | PTHR11476 | HISTIDYL-TRNA SYNTHETASE | 1 | 203 | 0 |
| 4 | g14000.t2 | PANTHER | PTHR11476:SF8 | HISTIDINE–TRNA LIGASE, CYTOPLASMIC | 1 | 203 | 0 |
| 1 | g14000.t2 | Pfam | PF13393 | Histidyl-tRNA synthetase | 7 | 89 | 0 |
| 2 | g14000.t2 | Pfam | PF03129 | Anticodon binding domain | 110 | 199 | 0 |
| 5 | g14000.t2 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 3 | 94 | 0 |
| 6 | g14000.t2 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 107 | 202 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
