General information for g14000.t4
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.t4 | TTS | g14000.t4 | 33944837 | 33944837 |
| chr_1 | g14000 | g14000.t4 | isoform | g14000.t4 | 33944910 | 33946974 |
| chr_1 | g14000 | g14000.t4 | exon | g14000.t4.exon1 | 33944910 | 33946355 |
| chr_1 | g14000 | g14000.t4 | cds | g14000.t4.CDS1 | 33944910 | 33946232 |
| chr_1 | g14000 | g14000.t4 | exon | g14000.t4.exon2 | 33946878 | 33946974 |
| chr_1 | g14000 | g14000.t4 | TSS | g14000.t4 | 33947054 | 33947054 |
Sequences
>g14000.t4 Gene=g14000 Length=1543
ATGAGTGAAAACCGAGAAGAAATTCAGGAACAAATAAAGGTTCAAGGTGATCTTGTGCGT
AAACTTAAAGCTGCCAAGGAATCGAAAGAAAAGGTGAATTGATGAAGAAGTTGCAAAGTT
ATTAGCATTGAAGGCAAAGCTAAATGAAAATGAACCAGCAGCGCCTTTAAAATTCACTCT
TAAAACGCCTAAAGGCACACGAGATTATGCTCCTGAGCAAATGACTCTTCGACAAAGTGT
TTTGAACACAATAGTATCTGTTTTTAAAAAGCACGGTGCTGACACTATAGATACACCGGT
TTTTGAATTAAAAGAAGTTTTAACTGGAAAATATGGTGAAGATTCTAAACTCATTTATGA
TCTTAAAGATCAAGGAGGAGAAATTTTGTCAATGCGTTATGATTTGACAGTACCTCTTGC
TCGTTATTTAGCAATGAATAAAGTATCAAATATCAAGAGATATCACATAGCAAAAGTTTA
CCGTCGTGACAATCCAGCAATGACAAAAGGAAGGTATCGCGAGTTTTACCAATGTGATTT
TGATATTGCTGGAACTTATGATCCTATGCTTCCTGATGCCGAATGTGTAAAAGTTGTCTC
TGAAATTTTATCATCTTTAGACATTGGTGCATTTGTTATTAAATTGAATCATCGTAAACT
TCTTGATGGAATGTTTGAAGCATGTGGCGTTCCGGCAGAGAAATTTCGCACAATTTGTTC
AGCTGTTGATAAGTTGGATAAATCACCATGGGAAGATGTCAAAAAAGAAATGATTGATGA
GAAAGGTTTAGATGATGCAACCGCTAATAAGATTGGTGAATATGTTCGATTGAATGGTGG
TGAAGAACTTGTCGATAAATTATTAACTGATGAAAAATTGAAGAAGGTGAAGTCAGCAGT
TGCGGGATTGGAAGACATGAAACTGTTGCTAAAATACTGTAAAATTTTCAATGTTATGCA
TCAAGTGCGTTTCGATTTGAGTCTTGCTAGAGGTCTCGACTATTATACTGGTGTTATTTA
TGAAGCTGTTCTTTTAAATCAAGAAAAGAAACGTAAAAAGGATGAAGAGACAGAAATTGG
ATCAGTCGCTGGTGGAGGACGTTATGATAATCTTGTTGGTATGTTCGATTCAAAAGGCAA
ACAAGTTCCTTGTGTTGGTGTTTCTATTGGTGTTGAAAGAGTTTTTGCAATTATTGAAGC
GAAGAATGCAGCAAACAAGACGAAAATAAGAACGAGTGAGATTCAAATCTTTGTAGCATC
AGCACATAAGGGATTGCATGAAAAGCGTTTAGAAATTCTTTCTAAATTATGGGATGGAGG
CATAAAAGCAGAACATTCCTATAAATCAAATCCAAAATTGCTAGCTCAGCTGCAATATTG
TGAAGAGCAGCAAATTCCTTTTGCATTGGTGCTCGGTGACAGTGAATTAGAACGTGGAGT
TATAAAATTACGTGATGTTGTAACACGTAAAGAAGAAGAAATTCCATTGGATAATTTGGT
TGAAGCAATTAAATGGCGTTTGAGTAATAAAGGTTATAACTAA
>g14000.t4 Gene=g14000 Length=440
MTLRQSVLNTIVSVFKKHGADTIDTPVFELKEVLTGKYGEDSKLIYDLKDQGGEILSMRY
DLTVPLARYLAMNKVSNIKRYHIAKVYRRDNPAMTKGRYREFYQCDFDIAGTYDPMLPDA
ECVKVVSEILSSLDIGAFVIKLNHRKLLDGMFEACGVPAEKFRTICSAVDKLDKSPWEDV
KKEMIDEKGLDDATANKIGEYVRLNGGEELVDKLLTDEKLKKVKSAVAGLEDMKLLLKYC
KIFNVMHQVRFDLSLARGLDYYTGVIYEAVLLNQEKKRKKDEETEIGSVAGGGRYDNLVG
MFDSKGKQVPCVGVSIGVERVFAIIEAKNAANKTKIRTSEIQIFVASAHKGLHEKRLEIL
SKLWDGGIKAEHSYKSNPKLLAQLQYCEEQQIPFALVLGDSELERGVIKLRDVVTRKEEE
IPLDNLVEAIKWRLSNKGYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g14000.t4 | CDD | cd00773 | HisRS-like_core | 1 | 326 | 0.000 |
| 9 | g14000.t4 | CDD | cd00859 | HisRS_anticodon | 340 | 431 | 0.000 |
| 7 | g14000.t4 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 1 | 336 | 0.000 |
| 6 | g14000.t4 | Gene3D | G3DSA:3.40.50.800 | - | 337 | 437 | 0.000 |
| 3 | g14000.t4 | PANTHER | PTHR11476 | HISTIDYL-TRNA SYNTHETASE | 1 | 436 | 0.000 |
| 8 | g14000.t4 | PIRSF | PIRSF001549 | His-tRNA_synth | 1 | 434 | 0.000 |
| 1 | g14000.t4 | Pfam | PF13393 | Histidyl-tRNA synthetase | 5 | 321 | 0.000 |
| 2 | g14000.t4 | Pfam | PF03129 | Anticodon binding domain | 342 | 431 | 0.000 |
| 11 | g14000.t4 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 1 | 325 | 11.423 |
| 4 | g14000.t4 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 1 | 326 | 0.000 |
| 5 | g14000.t4 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 339 | 433 | 0.000 |
| 12 | g14000.t4 | TIGRFAM | TIGR00442 | hisS: histidine–tRNA ligase | 2 | 422 | 0.000 |
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
- This transcript has been annotated with K01892 (histidyl-tRNA synthetase)
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. There were no conditions that were differentially expressed