General information for g13420.t1
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.t1 | isoform | g13420.t1 | 29970259 | 29973405 |
| chr_1 | g13420 | g13420.t1 | exon | g13420.t1.exon1 | 29970259 | 29970371 |
| chr_1 | g13420 | g13420.t1 | cds | g13420.t1.CDS1 | 29970259 | 29970371 |
| chr_1 | g13420 | g13420.t1 | exon | g13420.t1.exon2 | 29970437 | 29970567 |
| chr_1 | g13420 | g13420.t1 | cds | g13420.t1.CDS2 | 29970437 | 29970567 |
| chr_1 | g13420 | g13420.t1 | exon | g13420.t1.exon3 | 29970643 | 29970754 |
| chr_1 | g13420 | g13420.t1 | cds | g13420.t1.CDS3 | 29970643 | 29970754 |
| chr_1 | g13420 | g13420.t1 | exon | g13420.t1.exon4 | 29973381 | 29973405 |
| chr_1 | g13420 | g13420.t1 | cds | g13420.t1.CDS4 | 29973381 | 29973405 |
| chr_1 | g13420 | g13420.t1 | TSS | g13420.t1 | NA | NA |
| chr_1 | g13420 | g13420.t1 | TTS | g13420.t1 | NA | NA |
Sequences
>g13420.t1 Gene=g13420 Length=381
ATGTTAAGGATCATCATCATCATTGTAGCAGTAGCCACTAGTCGTGGAAGTGATGTTGAG
TTATTCGGAAATGAGATGGAAATGTCAATGAAACAGCGAAATCAAGCAAATGCTCGTGAA
CGCTATAGAACTCACAGTGTCAACTCAGCATTCAACACATTGCGATTACTGATTCCAACT
GAACCGAAAATCGAAAATTGTCAAAAATCGAAACTTTACGCTTGGCAAAATCTTACATTT
CTCATTCTCAATGCAACTCTTTCCATTGGAAATTCCACTTGTCGACAACCATGCTTTGAA
GTGAGCAGTAATAAAACTTTTCAACATGATTATCGATCAAAATCTGTACATATTTGTGTT
TCATCAGTCATATCATCATAA
>g13420.t1 Gene=g13420 Length=126
MLRIIIIIVAVATSRGSDVELFGNEMEMSMKQRNQANARERYRTHSVNSAFNTLRLLIPT
EPKIENCQKSKLYAWQNLTFLILNATLSIGNSTCRQPCFEVSSNKTFQHDYRSKSVHICV
SSVISS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13420.t1 | Gene3D | G3DSA:4.10.280.10 | HLH | 27 | 74 | 7.1E-12 |
| 2 | g13420.t1 | PANTHER | PTHR23349:SF42 | HELIX LOOP HELIX | 28 | 119 | 9.0E-12 |
| 3 | g13420.t1 | PANTHER | PTHR23349 | BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST | 28 | 119 | 9.0E-12 |
| 1 | g13420.t1 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 32 | 65 | 1.1E-6 |
| 8 | g13420.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 9 | g13420.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g13420.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 11 | g13420.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 7 | g13420.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 126 | - |
| 4 | g13420.t1 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 26 | 64 | 1.4E-7 |
| 5 | g13420.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
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