General information for g13450.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13450 is located on chr_1: 30215275..30216096 (+ 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 | g13450 | g13450.t2 | TSS | g13450.t2 | 30214213 | 30214213 |
| chr_1 | g13450 | g13450.t2 | isoform | g13450.t2 | 30214228 | 30216096 |
| chr_1 | g13450 | g13450.t2 | exon | g13450.t2.exon1 | 30214228 | 30214348 |
| chr_1 | g13450 | g13450.t2 | cds | g13450.t2.CDS1 | 30214228 | 30214348 |
| chr_1 | g13450 | g13450.t2 | exon | g13450.t2.exon2 | 30214406 | 30216096 |
| chr_1 | g13450 | g13450.t2 | cds | g13450.t2.CDS2 | 30214406 | 30216096 |
| chr_1 | g13450 | g13450.t2 | TTS | g13450.t2 | NA | NA |
Sequences
>g13450.t2 Gene=g13450 Length=1812
ATGTTGTCAGAAAAAATTTTGCAATTATTAAATTTAAACGAAATAAGTGGAGAAAAGAAT
TACTTGTTTAATGATTTTACTTTAAACTGGTCTTTCATTGACAAAATATTTTCCAATTCA
GACAAAAATCTTGATGACATTGACTCGTGCTTTAAATTAAAAGAATTGATTGATCCAATA
ATAATTAGTTCATATCAAGTTTTACATCATAAAAAGCTATTTATCGACTCATTAAAATTA
TTTACAAATTGGACATGTGCATCGATCATATTGGAAAACATTTTTAGAGAGTTTTGTACT
GATGAAAAAAGTTTCGCTCTAACAGGATTTTTAGTAGCGGTTACAATATTAGAATTTTCA
TTAGGAAATGTCTATGAAACGTACAATAAAACTAGCCCACCTCACTTACTTAAAGATGTA
TTGAATGAACTCCGATCGTGTTCTTACTTTCAAGGAAATCAAATTTTTATTCTACAAATT
CTTCTTGGTACAGCAAAATCGTGTAATTTAAGAAATATCGCATGGCATGGATTTATTGAA
TCATTACATCCTGCTTATCTCACATTCTTATTTGTTGTAATAATTTCATTTGGAAAACAA
TTAAAAGATTTAAAAATAATACCAAGATATCGCCACAATTTAAAATTGAAGTTTGAAATT
TCATCAATAGAAATGAATTATAAAGAAATTTTCCAAACGATGCAATGTAATCCTAAAGCA
TGGACTCAAATTTTATATTTTAAAAAAGAGAAAAAATTTAGAAATGGAATTTATCTTTTG
CTTCCACAAATTGAGAGTATTCTGAGATTCATTTATAGCAAAATCAACGAAGAGGAGGAT
GCAGTTACAGCTCAATTAAACAAGTATTATGTAATAATGGATTCAATATTCTATGAATAT
ATACTGTCAAATGATATTACACCTCTAATGATTGGGAAAATAACAAAAATTCAGGAAATG
GAAATTAGAAAGACTCATAAACGCAACAAGATGCTCACATTTATCCCACGATCAATTTAC
TTAATATATTATGATTTATTTTATGCCATCGATGGACCAAGATTGCGTGACAAATTGAGT
CATGGAGAAGTCATTATTGAAGATGATGATTTAGAGGATATTTTTAAAATTCTTTTAAAT
TTTGCATCAATCATAGTAAATTTTTATCAAAATCAAATTGTTGCTAAAAATTTTGTTTAT
GAGAGCAAATTCTTGAAAATTTTAATTTTTGTTAGAAATTTTAACATAACAAATCAATCT
GCAAAGCTCATATTTGATAAAATGGAAATTCCAAAGCTATTGATTACAGAAAAAATTAAT
TTTACTGAAATCGAAATTGAAAATGAAGAAGACGTAAAAATTTATTTTAGACCAGCTATA
GAAGCTCAAATTGTAAAATTGATGATGAAAATTTTAGAAAATTTTAATGAAGCTCTAGAA
TATTTCAAGAATTCTCTAATAGAACTTTTTCAACAATATGAAAAGAAAGAATTAAGCAGT
AGTCGTAGAAAAGTAGTTGAAAGTTTAATTAAATTTTTGCCAAATTTTTCAAACGGTTTT
CATGAAGTTTTACACGTGCAACAAAATATATATTTTACACTTCAACAATATGACAATACA
TTTGACAATGAAAACTGGAATAAGAAAATTATTAAACTTCTTAAGCAAACACTTCAAATC
ACAGAAGTTTATCTTAAACATTTTTCATCAAAAAATCGAAATTTTTTTGTAGCAAACACA
AAAACGTGTGAATTTTTGCAATTGTCGATCAAAAGTCAATATTTATTTCAAATTGAGAAC
ATAAATCAATAA
>g13450.t2 Gene=g13450 Length=603
MLSEKILQLLNLNEISGEKNYLFNDFTLNWSFIDKIFSNSDKNLDDIDSCFKLKELIDPI
IISSYQVLHHKKLFIDSLKLFTNWTCASIILENIFREFCTDEKSFALTGFLVAVTILEFS
LGNVYETYNKTSPPHLLKDVLNELRSCSYFQGNQIFILQILLGTAKSCNLRNIAWHGFIE
SLHPAYLTFLFVVIISFGKQLKDLKIIPRYRHNLKLKFEISSIEMNYKEIFQTMQCNPKA
WTQILYFKKEKKFRNGIYLLLPQIESILRFIYSKINEEEDAVTAQLNKYYVIMDSIFYEY
ILSNDITPLMIGKITKIQEMEIRKTHKRNKMLTFIPRSIYLIYYDLFYAIDGPRLRDKLS
HGEVIIEDDDLEDIFKILLNFASIIVNFYQNQIVAKNFVYESKFLKILIFVRNFNITNQS
AKLIFDKMEIPKLLITEKINFTEIEIENEEDVKIYFRPAIEAQIVKLMMKILENFNEALE
YFKNSLIELFQQYEKKELSSSRRKVVESLIKFLPNFSNGFHEVLHVQQNIYFTLQQYDNT
FDNENWNKKIIKLLKQTLQITEVYLKHFSSKNRNFFVANTKTCEFLQLSIKSQYLFQIEN
INQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13450.t2 | PANTHER | PTHR31701 | ENDOPLASMIC RETICULUM MEMBRANE-ASSOCIATED RNA DEGRADATION PROTEIN | 24 | 368 | 2.5E-36 |
| 3 | g13450.t2 | PANTHER | PTHR31701 | ENDOPLASMIC RETICULUM MEMBRANE-ASSOCIATED RNA DEGRADATION PROTEIN | 449 | 587 | 2.5E-36 |
| 1 | g13450.t2 | Pfam | PF13910 | Domain of unknown function (DUF4209) | 120 | 196 | 1.4E-11 |
| 5 | g13450.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 104 | - |
| 9 | g13450.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 105 | 125 | - |
| 7 | g13450.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 126 | 183 | - |
| 8 | g13450.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 201 | - |
| 4 | g13450.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 202 | 330 | - |
| 10 | g13450.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 350 | - |
| 6 | g13450.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 351 | 603 | - |
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 K25139 (endoplasmic reticulum membrane-associated RNA degradation protein)
Pathway
This gene does not belong to any 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.
