General information for g13420.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13420 is located on chr_1: 29970259..29973405 (- 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 | g13420 | g13420.t2 | isoform | g13420.t2 | 29970259 | 29970754 |
| chr_1 | g13420 | g13420.t2 | exon | g13420.t2.exon1 | 29970259 | 29970371 |
| chr_1 | g13420 | g13420.t2 | cds | g13420.t2.CDS1 | 29970259 | 29970371 |
| chr_1 | g13420 | g13420.t2 | exon | g13420.t2.exon2 | 29970437 | 29970567 |
| chr_1 | g13420 | g13420.t2 | cds | g13420.t2.CDS2 | 29970437 | 29970567 |
| chr_1 | g13420 | g13420.t2 | exon | g13420.t2.exon3 | 29970643 | 29970754 |
| chr_1 | g13420 | g13420.t2 | cds | g13420.t2.CDS3 | 29970643 | 29970704 |
| chr_1 | g13420 | g13420.t2 | TSS | g13420.t2 | NA | NA |
| chr_1 | g13420 | g13420.t2 | TTS | g13420.t2 | NA | NA |
Sequences
>g13420.t2 Gene=g13420 Length=356
TAGCAGTAGCCACTAGTCGTGGAAGTGATGTTGAGTTATTCGGAAATGAGATGGAAATGT
CAATGAAACAGCGAAATCAAGCAAATGCTCGTGAACGCTATAGAACTCACAGTGTCAACT
CAGCATTCAACACATTGCGATTACTGATTCCAACTGAACCGAAAATCGAAAATTGTCAAA
AATCGAAACTTTACGCTTGGCAAAATCTTACATTTCTCATTCTCAATGCAACTCTTTCCA
TTGGAAATTCCACTTGTCGACAACCATGCTTTGAAGTGAGCAGTAATAAAACTTTTCAAC
ATGATTATCGATCAAAATCTGTACATATTTGTGTTTCATCAGTCATATCATCATAA
>g13420.t2 Gene=g13420 Length=101
MEMSMKQRNQANARERYRTHSVNSAFNTLRLLIPTEPKIENCQKSKLYAWQNLTFLILNA
TLSIGNSTCRQPCFEVSSNKTFQHDYRSKSVHICVSSVISS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13420.t2 | Gene3D | G3DSA:4.10.280.10 | HLH | 3 | 50 | 0e+00 |
| 2 | g13420.t2 | PANTHER | PTHR23349:SF42 | HELIX LOOP HELIX | 5 | 95 | 0e+00 |
| 3 | g13420.t2 | PANTHER | PTHR23349 | BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST | 5 | 95 | 0e+00 |
| 1 | g13420.t2 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 7 | 40 | 6e-07 |
| 4 | g13420.t2 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 3 | 39 | 2e-07 |
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:0046983 | protein dimerization activity | MF |
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. There were no conditions that were differentially expressed