General information for g3969.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g3969 is located on chr_3: 29323854..29333743 (- 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_3 | g3969 | g3969.t1 | TTS | g3969.t1 | 29322391 | 29322391 |
| chr_3 | g3969 | g3969.t1 | isoform | g3969.t1 | 29322420 | 29323854 |
| chr_3 | g3969 | g3969.t1 | exon | g3969.t1.exon1 | 29322420 | 29323677 |
| chr_3 | g3969 | g3969.t1 | cds | g3969.t1.CDS1 | 29322420 | 29323677 |
| chr_3 | g3969 | g3969.t1 | exon | g3969.t1.exon2 | 29323736 | 29323854 |
| chr_3 | g3969 | g3969.t1 | cds | g3969.t1.CDS2 | 29323736 | 29323854 |
| chr_3 | g3969 | g3969.t1 | TSS | g3969.t1 | 29323887 | 29323887 |
Sequences
>g3969.t1 Gene=g3969 Length=1377
ATGCTGCGAAGATTTCAAAAAAATATTTTAACCAATTATATTCAAAGTAGAAGTTATTAT
AATTTACTTCGACTTAAAAGTCGTGGAGTGTTTCAAGAAGTATTTCCACATGAAGCAGAA
GGAAAAATTCAAGCTGAACTCGGTAAAAGTGAACAAACGATTTATGCAGGCTTCGATCCA
ACGAGTGATAGTCTTCATGTTGGTAATTTATTAGTAATAATAGGATTACTTCATGCACAA
CGTGGACAACATCGAACAATTGCATTGATAGGAGGTGCAACAGGAAAAATCGGAGATCCA
AGTGGAAGATCTAAAGAAAGAAATCTACTTGAAAACAATGTAATTGATCATAATTTAAAA
TCAATAAGCATTCAAATTAAAAAAATTTTTGATAATCATCGAGAATATTTTTGGGAGAAA
CAAAATCAAAAGAAAGAAGAATTGAAAGAGTTGCTAATTGTTAATAATGCTGATTGGTAT
AGTGACATTAGTTTTATCGACTTTATTTCTAAAGTAGGCAGACATTTTCGACTTGGTCAA
ATGTTATCAAGAGCATCAGTTAGAAGTAGACTGGAAAGTGAAGAAGGAATGAGTTTTACA
GAATTTACTTATCAAGTATTTCAAGCTTATGATTGGCTACAATTATTTCAAAAATATAAT
TGTCGTTATCAAATGGGAGGTCTTGATCAGATGGGAAATCTAATGACTGGATGTGAATTT
ATTACAAGAGTTTTAAAGAAACAAGCATACGGCATTACATTACCAATTATAACTAATGAA
GAAGGTAACAAATTTGGTAAATCAGCTGGAAATGCTGTTTGGCTTGATGCCAATAAAACA
TCAGAATTTGGATTTTATCAGTTTTTCTTGAGGCAACCTGATACAGAAGCAGAAAAATTA
TTTAAACTTTTCTCTCTTCTTCGAACGAATGAAGTTTTTGATCAAATTGATAAACATAAA
CGAGCACCTGAATTAAGAGGACTTCAAATAGCATTAGCCGATCAATTGACTCTATTAATT
CATGGTGAAAAGGGTTTAGAGAAGGCTAAAAAAATTTCAAACGCCTTATATAATGGTGAT
GTTCATGCATTAGGTTCGATGAATAAAAACGAAGTACAAGAGGTATTTTCAGGAGCACCC
TATAAAGAACTCATTCTTGAACCAGGAATGACCATTTTAAATATTGGTATGAGGGTTGGT
TGCTTTAAACATGAAAATGATGCTAAAAGAATAATATCAGCTGGAGGATTTTACATTAAT
ATGAAACGCTCAAATAATCCTTCTGAAATTTTAACACCAAATGTTCATATTTTACCTAAT
GACATTACACTTATAAGAGTAGGAAAAAGAAATTTCTATATTATTAAGTGGGTATAA
>g3969.t1 Gene=g3969 Length=458
MLRRFQKNILTNYIQSRSYYNLLRLKSRGVFQEVFPHEAEGKIQAELGKSEQTIYAGFDP
TSDSLHVGNLLVIIGLLHAQRGQHRTIALIGGATGKIGDPSGRSKERNLLENNVIDHNLK
SISIQIKKIFDNHREYFWEKQNQKKEELKELLIVNNADWYSDISFIDFISKVGRHFRLGQ
MLSRASVRSRLESEEGMSFTEFTYQVFQAYDWLQLFQKYNCRYQMGGLDQMGNLMTGCEF
ITRVLKKQAYGITLPIITNEEGNKFGKSAGNAVWLDANKTSEFGFYQFFLRQPDTEAEKL
FKLFSLLRTNEVFDQIDKHKRAPELRGLQIALADQLTLLIHGEKGLEKAKKISNALYNGD
VHALGSMNKNEVQEVFSGAPYKELILEPGMTILNIGMRVGCFKHENDAKRIISAGGFYIN
MKRSNNPSEILTPNVHILPNDITLIRVGKRNFYIIKWV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3969.t1 | CDD | cd00805 | TyrRS_core | 52 | 339 | 4.55697E-102 |
| 11 | g3969.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 4 | 256 | 6.7E-93 |
| 10 | g3969.t1 | Gene3D | G3DSA:1.10.240.10 | - | 257 | 362 | 4.9E-32 |
| 12 | g3969.t1 | Gene3D | G3DSA:3.10.290.10 | - | 363 | 458 | 2.0E-20 |
| 2 | g3969.t1 | PANTHER | PTHR11766:SF0 | TYROSINE–TRNA LIGASE, MITOCHONDRIAL | 20 | 458 | 4.2E-166 |
| 3 | g3969.t1 | PANTHER | PTHR11766 | TYROSYL-TRNA SYNTHETASE | 20 | 458 | 4.2E-166 |
| 5 | g3969.t1 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 64 | 86 | 8.5E-20 |
| 7 | g3969.t1 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 196 | 211 | 8.5E-20 |
| 6 | g3969.t1 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 217 | 239 | 8.5E-20 |
| 4 | g3969.t1 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 250 | 262 | 8.5E-20 |
| 1 | g3969.t1 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 51 | 357 | 2.0E-64 |
| 14 | g3969.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 60 | 70 | - |
| 9 | g3969.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 22 | 357 | 7.74E-80 |
| 8 | g3969.t1 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 366 | 457 | 2.67E-11 |
| 15 | g3969.t1 | TIGRFAM | TIGR00234 | tyrS: tyrosine–tRNA ligase | 24 | 457 | 2.7E-91 |
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:0003723 | RNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004831 | tyrosine-tRNA ligase activity | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0006437 | tyrosyl-tRNA aminoacylation | BP |
KEGG
Orthology
- This transcript has been annotated with K01866 (tyrosyl-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.
