General information for g3376.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable proline–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g3376 is located on chr_3: 24965665..24967852 (- 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 | g3376 | g3376.t12 | TTS | g3376.t12 | 24964235 | 24964235 |
| chr_3 | g3376 | g3376.t12 | isoform | g3376.t12 | 24964293 | 24965665 |
| chr_3 | g3376 | g3376.t12 | exon | g3376.t12.exon1 | 24964293 | 24965210 |
| chr_3 | g3376 | g3376.t12 | cds | g3376.t12.CDS1 | 24964293 | 24965210 |
| chr_3 | g3376 | g3376.t12 | exon | g3376.t12.exon2 | 24965266 | 24965402 |
| chr_3 | g3376 | g3376.t12 | cds | g3376.t12.CDS2 | 24965266 | 24965379 |
| chr_3 | g3376 | g3376.t12 | exon | g3376.t12.exon3 | 24965570 | 24965665 |
| chr_3 | g3376 | g3376.t12 | TSS | g3376.t12 | 24965667 | 24965667 |
Sequences
>g3376.t12 Gene=g3376 Length=1151
ATGAACCGCTTGTCAAAAATATTTTTTCCACAACTTATTGTGCCGAAAAATGCAATTGTC
AAAAGTCATGAAGTACAACAATCTAAAAGTCAAAAGAAATCGATGGTCAAAAAATTACTA
TGCCCACATTAACATCAGCAGACTTATGGAAAAAATCTGGGAGATTTGAAAATGCAGTAA
CTGAATTGATGACAGTCAATGATAGGCATAATAGACTTCAAATTCTTAGTCCTACACATG
AGGAATCAGTGACAAACTTAATTGCATCTATTTCTCCAGTCTCTTACAAAAGCTTTCCTC
TTCGTCTTTATCAAATTACACCTAAATTTCGAGATGAGTTAAGACCAAAATTTGGATTAT
TGAGAGCAAAAGAGTTTTTAATGAAGGATATGTACACCTTTGATATTGGATTAAATGAGG
CTAAAAAGACATATGATGAAGTTAATGAACAATATGTCAAAATTTTCAATCATTTGAATG
TATCCTTTATAAAAATTGGCGCTGATACTGGTAATATGGGCGGAAATATTTCTCATGAAT
TTCATATAGCAAGTTCTATTGGCGAAGATTCAATCATTTCATGTACATCTTGTTCAAAAG
CTATTAATGTTGAATTGGCAAAAGATGGAAAAATATGTGAACAATGTAAAATTGATGATC
TTAAACGTCAGCAAGGAATTGAAATTGGTCACACATTTATTCTTGAAGATAGGTATTCAA
AAGTGTTAAATGCTACATTTTTAAATAAAACTGGAAAACCAGAAAATATTCAAATGGGTT
GTTATGGAATCGGTGTGACTCGTCTTATAGCAGCAGTAATTGAACTTTTCTCAAACGAAA
ATGAAATCAGATGGTCAGATGCAATAGCACCATACAAAATTTGTATTATTCCACCAAAGG
AAGGAAGCAAAGAAGAGGAGTCTGTTAAGCATTTAAGCAATGAAATTTATCATTATCTGA
CTACTAATTCATCACAACTTGCGGATGATATTATTGTAGATGATCGAACACACATGACAA
TTGGTAAACGGTTGAAAGAGATCAAGAAACTTGGAATACCTTATATTATAGTTATTGGAT
CAAAATCAGCTGATATAAGTTCTACAATAGAAGTTCATAATTTGAGAGAAAATGTAGCCA
TAGATATGAGT
>g3376.t12 Gene=g3376 Length=344
MPTLTSADLWKKSGRFENAVTELMTVNDRHNRLQILSPTHEESVTNLIASISPVSYKSFP
LRLYQITPKFRDELRPKFGLLRAKEFLMKDMYTFDIGLNEAKKTYDEVNEQYVKIFNHLN
VSFIKIGADTGNMGGNISHEFHIASSIGEDSIISCTSCSKAINVELAKDGKICEQCKIDD
LKRQQGIEIGHTFILEDRYSKVLNATFLNKTGKPENIQMGCYGIGVTRLIAAVIELFSNE
NEIRWSDAIAPYKICIIPPKEGSKEEESVKHLSNEIYHYLTTNSSQLADDIIVDDRTHMT
IGKRLKEIKKLGIPYIIVIGSKSADISSTIEVHNLRENVAIDMS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3376.t12 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 1 | 240 | 0.0000000 |
| 10 | g3376.t12 | Gene3D | G3DSA:3.40.50.800 | - | 241 | 344 | 0.0000000 |
| 3 | g3376.t12 | PANTHER | PTHR42753:SF2 | PROLINE–TRNA LIGASE, MITOCHONDRIAL-RELATED | 1 | 336 | 0.0000000 |
| 4 | g3376.t12 | PANTHER | PTHR42753 | MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER | 1 | 336 | 0.0000000 |
| 5 | g3376.t12 | PRINTS | PR01046 | Prolyl-tRNA synthetase signature | 34 | 45 | 0.0000000 |
| 7 | g3376.t12 | PRINTS | PR01046 | Prolyl-tRNA synthetase signature | 65 | 73 | 0.0000000 |
| 6 | g3376.t12 | PRINTS | PR01046 | Prolyl-tRNA synthetase signature | 75 | 86 | 0.0000000 |
| 1 | g3376.t12 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 25 | 235 | 0.0000000 |
| 2 | g3376.t12 | Pfam | PF03129 | Anticodon binding domain | 253 | 337 | 0.0000003 |
| 12 | g3376.t12 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 1 | 251 | 15.8160000 |
| 8 | g3376.t12 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 1 | 256 | 0.0000000 |
| 9 | g3376.t12 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 242 | 324 | 0.0000000 |
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:0006433 | prolyl-tRNA aminoacylation | BP |
| GO:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0004827 | proline-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01881 (prolyl-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.
