General information for g13409.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13409 is located on chr_1: 29888360..29889337 (- 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 | g13409 | g13409.t4 | TTS | g13409.t4 | 29885566 | 29885566 |
| chr_1 | g13409 | g13409.t4 | isoform | g13409.t4 | 29886118 | 29887234 |
| chr_1 | g13409 | g13409.t4 | exon | g13409.t4.exon1 | 29886118 | 29886625 |
| chr_1 | g13409 | g13409.t4 | cds | g13409.t4.CDS1 | 29886521 | 29886625 |
| chr_1 | g13409 | g13409.t4 | exon | g13409.t4.exon2 | 29886688 | 29886802 |
| chr_1 | g13409 | g13409.t4 | cds | g13409.t4.CDS2 | 29886688 | 29886802 |
| chr_1 | g13409 | g13409.t4 | exon | g13409.t4.exon3 | 29886953 | 29887132 |
| chr_1 | g13409 | g13409.t4 | cds | g13409.t4.CDS3 | 29886953 | 29887011 |
| chr_1 | g13409 | g13409.t4 | exon | g13409.t4.exon4 | 29887227 | 29887234 |
| chr_1 | g13409 | g13409.t4 | TSS | g13409.t4 | NA | NA |
Sequences
>g13409.t4 Gene=g13409 Length=811
CCTCAGAGTGGTGAGTTGCCGTGCGAACGATGGAATCCAACTCAAAATGTCCGCACCATT
CTCCTCTCTGTAATCTCATTGCTCAATGAACCCAACACATTTTCACCAGCTAATGTAGAC
GCAAGTGTTATGTACAGAAGATGGCGTGAATCAAATGGTCGCGATAACGAATATCCAAAC
ATAATCAGGAAACAAGCGTTACAAGCTAAGTTAGAAGCTGAAAAAGAAGGAATTGTTGTT
CCATTAACATTAGAGGAATATTGCCTGAAACCTAAAACGAACCCAAATAATCAGGAACCT
CAACTCGATATGACAGACTTTTATGACGATTTCGATGATGATGAGTGTAGCGAATCTGAA
ACAGAATCACAAAATGGTGATGGAGAAGATTCGGGGAACGCTGAATAAATGCATCACTTA
ATTTTAGACGTTCGTTTGCGATAAAGTTGTTTTCGAAAAAAGTGAAATTTCTTATTAAGT
TAGCAATCAAACAGCAAAAAACATCAAATAATATTTTACAAAAAATTGAAACTGAAAGGT
ATTTAAGCAGTGTGAATAAGTAAAGAGTAAAAACCGAAGTTGAAATTAGAGTTTATTAGT
TCAAGTAACTCAAAACTTTGTCACGAGTTAACTTGCACTAATACTACCTACATTTGAAGA
ATTAAGATCCTTTCTATATATTAAAATTACTATTATCGATAGAAACAGGCTAAGTTTGAA
ACAAATTTCAATTAAGAAAAAAAAATTTTAACTGAAAAATACAATTATTTACAACAAAAC
ATTAATGAAAGGTACATTATCCCCTTCAAAA
>g13409.t4 Gene=g13409 Length=92
MYRRWRESNGRDNEYPNIIRKQALQAKLEAEKEGIVVPLTLEEYCLKPKTNPNNQEPQLD
MTDFYDDFDDDECSESETESQNGDGEDSGNAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g13409.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 92 | - |
| 3 | g13409.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 82 | - |
| 1 | g13409.t4 | PANTHER | PTHR24067:SF148 | UBIQUITIN-CONJUGATING ENZYME E2 R2 | 2 | 77 | 2.2E-14 |
| 2 | g13409.t4 | PANTHER | PTHR24067 | UBIQUITIN-CONJUGATING ENZYME E2 | 2 | 77 | 2.2E-14 |
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.
