General information for g3578.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3578 is located on chr_3: 26527032..26528478 (+ 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 | g3578 | g3578.t11 | isoform | g3578.t11 | 26523634 | 26525503 |
| chr_3 | g3578 | g3578.t11 | exon | g3578.t11.exon1 | 26523634 | 26524555 |
| chr_3 | g3578 | g3578.t11 | exon | g3578.t11.exon2 | 26524614 | 26524735 |
| chr_3 | g3578 | g3578.t11 | exon | g3578.t11.exon3 | 26524805 | 26525260 |
| chr_3 | g3578 | g3578.t11 | cds | g3578.t11.CDS1 | 26525096 | 26525260 |
| chr_3 | g3578 | g3578.t11 | exon | g3578.t11.exon4 | 26525336 | 26525503 |
| chr_3 | g3578 | g3578.t11 | cds | g3578.t11.CDS2 | 26525336 | 26525503 |
| chr_3 | g3578 | g3578.t11 | TSS | g3578.t11 | NA | NA |
| chr_3 | g3578 | g3578.t11 | TTS | g3578.t11 | NA | NA |
Sequences
>g3578.t11 Gene=g3578 Length=1668
TTTATTGAGTCAAAAGATTCATTTTAAAAAATTTTAGCATTGAATTTATTAAATATTTGA
AGTTCGTTATAGCGTTTGAATCAAAAGTCATTTTTTACACGATGTATTCTTTCAAGATTT
TGTTGTGCTATCATTCGTTCTCCTTTTGATTTTTTACCAATTCCAAGCTTTGGTAATCCT
CTATTTAATCCTTCAAGTAGAACACAAGCTTTGCAAGGTTGACAAGATGACACAAATCCA
CATGTTTGACATATATCAAGAACAGGCTTTTTTATGTTCTCTTTAAATTGAATTTGTTCT
CCAGAATGTATAATATCCATTATTACTGAAGGTCTAATTTTCTCTAAATCTTTCAGAAAC
ATTCTTGCATGACCACGATAAGCATTTGGAGCAAATATACATTCTGTTGAAAAGTATACG
AGTTTTTTGAAATGAGCATACATTACAATCTCCTTTTCATATGTGTATTTAAGAGGTTTT
ACTCGAGGAATAGCATCTTCGTTGCTGTGAGTTTTGATCTTTGTACATCGTCTCAATCTA
ACCATATCTCCTCTTAGAATGTTCATCAAAACTGTCTCGGCAATGTCATCTGCATTATGT
CCTGTTGCTACGCAGTCTACTTCAAGCATTTTAGCTCCTCTATCGAGAGCTTGTCGTCTA
AAGACACCACAGAATGTACAGTTATTAGTTTTTCCAATCACTGAAACTACCTTATCCATC
GTCCAACCATATAATTCTTCGTACGATAAAATTTTCAGCTCCATTCCATAATCATCTCTA
TTTTTCTTTACAGTTTCAAGAGAATCATCTCTATATCCAGTAATTCCTTCATCAATTGAT
AATAGAACAATTTTCAAATTATATTTATATCGTTCATTTAGTAATTTCAGTACATAAGCT
AAAACTGTTGAATCTTTTCCACAATATTACCTATTGCTACTTTATCACCACTTTTAAAGA
GTTGTCCTTTTGTAATTGTTTCATGAATTTCACATTCAAATGCTGTGAAGAAACATTCTT
TACAAAGTGCATCGCCAGTTTTTGCCTTTAAAATGGCTTTATTTCCACAGTTGGCTTTAC
ATAAAACCATGATTTTTAATATTATTTTATAAAATGTTTTCACTTGTTTACTTTTTCGTT
TAACCCTATTTTTGTAGTCGAAACTTTGAGATTATTCCTCATCAAAAAAAATTTTGTAGG
GTCTTACTGGAATTTAAAAAAAATATTGAGAAAATTGTATAAAATTGCATCATCCAATAG
TGTTAATATATAAAGGAATAATATTCTATTAACACTTATTAGAGTTTGTGAAATTCAGTA
TAATATCAATTAAAAATGACTAATGTAAAAACTGATGAAGCTGCAAACGAGGAAGTTGTT
GAAAAAAGTGCAAAACAACTCGAGAAAGAAGCTAAAAAAGCTGCTAAATTAGCTAAGCTT
CAAGAAAAACAAGCAAAACAGGCTACTCAACAAGCAAATACAGCACCTAAGGAAAAAGAG
AAAAAAGCTAAATCTGTAGTGAAAGACATTATTTATGAAGGAAATTCAAAGGATGGTGAA
AAGAAGGATTTATCTGGACCTATGCCAGAAGCTTACTCGCCTCAATACGTTGAAGCAGCG
TGGTATTCTTGGTGGGAGAAACAAGGATTTTTCAAGCCGGAATATTCT
>g3578.t11 Gene=g3578 Length=111
MTNVKTDEAANEEVVEKSAKQLEKEAKKAAKLAKLQEKQAKQATQQANTAPKEKEKKAKS
VVKDIIYEGNSKDGEKKDLSGPMPEAYSPQYVEAAWYSWWEKQGFFKPEYS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3578.t11 | Coils | Coil | Coil | 12 | 46 | - |
| 4 | g3578.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 61 | - |
| 3 | g3578.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 35 | - |
| 1 | g3578.t11 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 11 | 110 | 1.2E-27 |
| 2 | g3578.t11 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 11 | 110 | 1.2E-27 |
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.
