General information for g14000.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histidine–tRNA ligase.
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.t1 | TTS | g14000.t1 | 33944837 | 33944837 |
| chr_1 | g14000 | g14000.t1 | isoform | g14000.t1 | 33944910 | 33946974 |
| chr_1 | g14000 | g14000.t1 | exon | g14000.t1.exon1 | 33944910 | 33946355 |
| chr_1 | g14000 | g14000.t1 | cds | g14000.t1.CDS1 | 33944910 | 33946355 |
| chr_1 | g14000 | g14000.t1 | exon | g14000.t1.exon2 | 33946882 | 33946974 |
| chr_1 | g14000 | g14000.t1 | cds | g14000.t1.CDS2 | 33946882 | 33946974 |
| chr_1 | g14000 | g14000.t1 | TSS | g14000.t1 | 33947054 | 33947054 |
Sequences
>g14000.t1 Gene=g14000 Length=1539
ATGAGTGAAAACCGAGAAGAAATTCAGGAACAAATAAAGGTTCAAGGTGATCTTGTGCGT
AAACTTAAAGCTGCCAAGGAATCGAAAGAAAAGATTGATGAAGAAGTTGCAAAGTTATTA
GCATTGAAGGCAAAGCTAAATGAAAATGAACCAGCAGCGCCTTTAAAATTCACTCTTAAA
ACGCCTAAAGGCACACGAGATTATGCTCCTGAGCAAATGACTCTTCGACAAAGTGTTTTG
AACACAATAGTATCTGTTTTTAAAAAGCACGGTGCTGACACTATAGATACACCGGTTTTT
GAATTAAAAGAAGTTTTAACTGGAAAATATGGTGAAGATTCTAAACTCATTTATGATCTT
AAAGATCAAGGAGGAGAAATTTTGTCAATGCGTTATGATTTGACAGTACCTCTTGCTCGT
TATTTAGCAATGAATAAAGTATCAAATATCAAGAGATATCACATAGCAAAAGTTTACCGT
CGTGACAATCCAGCAATGACAAAAGGAAGGTATCGCGAGTTTTACCAATGTGATTTTGAT
ATTGCTGGAACTTATGATCCTATGCTTCCTGATGCCGAATGTGTAAAAGTTGTCTCTGAA
ATTTTATCATCTTTAGACATTGGTGCATTTGTTATTAAATTGAATCATCGTAAACTTCTT
GATGGAATGTTTGAAGCATGTGGCGTTCCGGCAGAGAAATTTCGCACAATTTGTTCAGCT
GTTGATAAGTTGGATAAATCACCATGGGAAGATGTCAAAAAAGAAATGATTGATGAGAAA
GGTTTAGATGATGCAACCGCTAATAAGATTGGTGAATATGTTCGATTGAATGGTGGTGAA
GAACTTGTCGATAAATTATTAACTGATGAAAAATTGAAGAAGGTGAAGTCAGCAGTTGCG
GGATTGGAAGACATGAAACTGTTGCTAAAATACTGTAAAATTTTCAATGTTATGCATCAA
GTGCGTTTCGATTTGAGTCTTGCTAGAGGTCTCGACTATTATACTGGTGTTATTTATGAA
GCTGTTCTTTTAAATCAAGAAAAGAAACGTAAAAAGGATGAAGAGACAGAAATTGGATCA
GTCGCTGGTGGAGGACGTTATGATAATCTTGTTGGTATGTTCGATTCAAAAGGCAAACAA
GTTCCTTGTGTTGGTGTTTCTATTGGTGTTGAAAGAGTTTTTGCAATTATTGAAGCGAAG
AATGCAGCAAACAAGACGAAAATAAGAACGAGTGAGATTCAAATCTTTGTAGCATCAGCA
CATAAGGGATTGCATGAAAAGCGTTTAGAAATTCTTTCTAAATTATGGGATGGAGGCATA
AAAGCAGAACATTCCTATAAATCAAATCCAAAATTGCTAGCTCAGCTGCAATATTGTGAA
GAGCAGCAAATTCCTTTTGCATTGGTGCTCGGTGACAGTGAATTAGAACGTGGAGTTATA
AAATTACGTGATGTTGTAACACGTAAAGAAGAAGAAATTCCATTGGATAATTTGGTTGAA
GCAATTAAATGGCGTTTGAGTAATAAAGGTTATAACTAA
>g14000.t1 Gene=g14000 Length=512
MSENREEIQEQIKVQGDLVRKLKAAKESKEKIDEEVAKLLALKAKLNENEPAAPLKFTLK
TPKGTRDYAPEQMTLRQSVLNTIVSVFKKHGADTIDTPVFELKEVLTGKYGEDSKLIYDL
KDQGGEILSMRYDLTVPLARYLAMNKVSNIKRYHIAKVYRRDNPAMTKGRYREFYQCDFD
IAGTYDPMLPDAECVKVVSEILSSLDIGAFVIKLNHRKLLDGMFEACGVPAEKFRTICSA
VDKLDKSPWEDVKKEMIDEKGLDDATANKIGEYVRLNGGEELVDKLLTDEKLKKVKSAVA
GLEDMKLLLKYCKIFNVMHQVRFDLSLARGLDYYTGVIYEAVLLNQEKKRKKDEETEIGS
VAGGGRYDNLVGMFDSKGKQVPCVGVSIGVERVFAIIEAKNAANKTKIRTSEIQIFVASA
HKGLHEKRLEILSKLWDGGIKAEHSYKSNPKLLAQLQYCEEQQIPFALVLGDSELERGVI
KLRDVVTRKEEEIPLDNLVEAIKWRLSNKGYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g14000.t1 | CDD | cd00773 | HisRS-like_core | 72 | 398 | 2.50551E-105 |
| 14 | g14000.t1 | CDD | cd00859 | HisRS_anticodon | 412 | 503 | 1.03465E-25 |
| 13 | g14000.t1 | Coils | Coil | Coil | 22 | 49 | - |
| 11 | g14000.t1 | Gene3D | G3DSA:1.10.287.10 | - | 3 | 55 | 4.1E-18 |
| 12 | g14000.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 56 | 408 | 1.4E-161 |
| 10 | g14000.t1 | Gene3D | G3DSA:3.40.50.800 | - | 409 | 509 | 3.2E-29 |
| 6 | g14000.t1 | Hamap | MF_00127 | Histidine–tRNA ligase [hisS]. | 57 | 504 | 23.832239 |
| 4 | g14000.t1 | PANTHER | PTHR11476 | HISTIDYL-TRNA SYNTHETASE | 4 | 507 | 4.0E-227 |
| 5 | g14000.t1 | PANTHER | PTHR11476:SF8 | HISTIDINE–TRNA LIGASE, CYTOPLASMIC | 4 | 507 | 4.0E-227 |
| 2 | g14000.t1 | Pfam | PF00458 | WHEP-TRS domain | 8 | 48 | 3.3E-15 |
| 1 | g14000.t1 | Pfam | PF13393 | Histidyl-tRNA synthetase | 64 | 393 | 2.6E-44 |
| 3 | g14000.t1 | Pfam | PF03129 | Anticodon binding domain | 414 | 503 | 2.9E-15 |
| 18 | g14000.t1 | ProSiteProfiles | PS51185 | WHEP-TRS domain profile. | 4 | 60 | 12.191 |
| 19 | g14000.t1 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 33 | 397 | 11.634 |
| 16 | g14000.t1 | SMART | SM00991 | WHEP_TRS_a_2_a_3_a | 8 | 63 | 7.3E-16 |
| 9 | g14000.t1 | SUPERFAMILY | SSF47060 | S15/NS1 RNA-binding domain | 6 | 50 | 2.16E-11 |
| 7 | g14000.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 59 | 398 | 4.38E-80 |
| 8 | g14000.t1 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 411 | 505 | 4.25E-20 |
| 17 | g14000.t1 | TIGRFAM | TIGR00442 | hisS: histidine–tRNA ligase | 60 | 494 | 4.0E-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:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0006427 | histidyl-tRNA aminoacylation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
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.
