General information for g13472.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13472 is located on chr_1: 30356217..30357285 (+ 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 | g13472 | g13472.t3 | TSS | g13472.t3 | 30355956 | 30355956 |
| chr_1 | g13472 | g13472.t3 | isoform | g13472.t3 | 30355985 | 30356992 |
| chr_1 | g13472 | g13472.t3 | exon | g13472.t3.exon1 | 30355985 | 30356143 |
| chr_1 | g13472 | g13472.t3 | cds | g13472.t3.CDS1 | 30355985 | 30356143 |
| chr_1 | g13472 | g13472.t3 | exon | g13472.t3.exon2 | 30356215 | 30356349 |
| chr_1 | g13472 | g13472.t3 | cds | g13472.t3.CDS2 | 30356215 | 30356349 |
| chr_1 | g13472 | g13472.t3 | exon | g13472.t3.exon3 | 30356672 | 30356791 |
| chr_1 | g13472 | g13472.t3 | cds | g13472.t3.CDS3 | 30356672 | 30356791 |
| chr_1 | g13472 | g13472.t3 | exon | g13472.t3.exon4 | 30356858 | 30356992 |
| chr_1 | g13472 | g13472.t3 | cds | g13472.t3.CDS4 | 30356858 | 30356992 |
| chr_1 | g13472 | g13472.t3 | TTS | g13472.t3 | 30357281 | 30357281 |
Sequences
>g13472.t3 Gene=g13472 Length=549
ATGATTGCAATAATAAAAAGATTTTTTCTGTTTTTGTTGAGGATTTTACGACGAGCACTA
TGTTGTTTTAGCAGAAAAAGACTTGATTCGGGATCACATTATGAAGATCGATTGGAAGTA
GTTGTGAGCGATAGTCCAAATTATAGTAAAAAATCAAATATGGAACGTGATTGGAATTCG
TGGGATGATAAACCGAGGACTGTAGAAGAGCACATTGAACAGTATCGTGAGAATTTAGTT
AAACCGAAGGAACCAGAATCAGTAGATGTTGTTGAGACACTTGATCTATTTGCGGATATG
ACACCACAAATAAAGAAGCAGAAGAAAGTTTTTATAAATCAAGGAGGAAACAGCAATAAT
TTTAATAATTTCTCACGTCTTGAAGCAACTGCAGTTGCTGAAATTCCCACAACAAATGAA
CTAGAAGACTGGAATGAGGAAACAAATCAAGCTGGCTGGACTGAAATTGATGATCAAAAT
ACAAAGCAGCTAATTAGAGAAACGAGAAAGGAAATGCGAGCAGCAAAACATAAGCAAAAT
TTTAGATAG
>g13472.t3 Gene=g13472 Length=182
MIAIIKRFFLFLLRILRRALCCFSRKRLDSGSHYEDRLEVVVSDSPNYSKKSNMERDWNS
WDDKPRTVEEHIEQYRENLVKPKEPESVDVVETLDLFADMTPQIKKQKKVFINQGGNSNN
FNNFSRLEATAVAEIPTTNELEDWNEETNQAGWTEIDDQNTKQLIRETRKEMRAAKHKQN
FR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g13472.t3 | PANTHER | PTHR15208 | RECEPTOR-BINDING CANCER ANTIGEN EXPRESSED ON SISO CELLS CANCER ASSOCIATED SURFACE ANTIGEN RCAS1 ESTROGEN RECEPTOR-BINDING FRAGMENT- ASSOCIATED GENE 9 PROTEIN | 5 | 179 | 1.4E-26 |
| 8 | g13472.t3 | PIRSF | PIRSF034247 | RCAS1 | 5 | 181 | 6.1E-9 |
| 4 | g13472.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 5 | g13472.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 6 | g13472.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 7 | g13472.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 3 | g13472.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 182 | - |
| 2 | g13472.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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 transcript has been annotated with K22455 (estrogen receptor-binding fragment-associated gene 9 protein)
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.
