General information for g12710.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Translocon-associated protein subunit alpha.
Parent gene
- The parent gene g12710 is located on chr_1: 25414443..25417609 (- 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 | g12710 | g12710.t16 | TTS | g12710.t16 | 25414039 | 25414039 |
| chr_1 | g12710 | g12710.t16 | isoform | g12710.t16 | 25414098 | 25415531 |
| chr_1 | g12710 | g12710.t16 | exon | g12710.t16.exon1 | 25414098 | 25415043 |
| chr_1 | g12710 | g12710.t16 | cds | g12710.t16.CDS1 | 25414443 | 25414949 |
| chr_1 | g12710 | g12710.t16 | exon | g12710.t16.exon2 | 25415101 | 25415313 |
| chr_1 | g12710 | g12710.t16 | exon | g12710.t16.exon3 | 25415471 | 25415531 |
| chr_1 | g12710 | g12710.t16 | TSS | g12710.t16 | 25415638 | 25415638 |
Sequences
>g12710.t16 Gene=g12710 Length=1220
ATGAAGCATTCATTGCTATTAGTTCTTCTCATTTTACCTGCATTTCTATTTATTTTTGAT
GCAAAGTGTTTGTTAGAGCAAATGAAGACGAAATTGATGAGGATTTAGTTGATGTCGAAA
ATGAAGGTGATGCAGATGAAGCAAGTGAAAGTGCGCTGACTGGCGATGATGTGGAGGCAG
ATGAGACTGGTGAAAGTACGAAATCTCCTGATGCTGACACTCAATTGCTCTTTGTTCGAC
CACTTTATACACCAGGATCACAACTTGAATTACCTGGCGGTGTTCCAGTAGAGTTCTTAA
TTGGCTTCTTAAATAAAGGCAAAAATGATTTCATTATTGAGAGTGTTGAAGCTTCATTCC
GTTATCCAATGGATTTCACTTACTACATTCAAAATTTCTCAGCACTTGCATATAACCGTG
AAGTTAAATCAGAGAGTGAAGCAACTGTATCATACTCATTCCTTCCATCAGAACAATTTG
CTGGTCGTCCTTTTGGTTTGAATATTGCCATTAGTTATCGTGATTCAACTGGTGCAGGTT
TTATGGAAGCAGTTTTCAATGAAACTGTTCTCATCACAGAATTAGATGAAGGTCTTGATG
GCGAAACATTCTTTTTATATGTGTTCTTTGCAGCTATTTTTGTTTTACTTCTTGTTGTTG
GACAACAATTCCTCGGTTCAATTGGCAAGAAGAAACGTTCACAAAACATTCGTAAGCAAG
TTGAGACTGGTACATCAAATAACACCGATATTGATTATGAATGGCTTCCTGCTCAAACAA
TTAGAAATTTACAAAATTCACCAAATGGCAAAGGAAAAATCTCGCCAAAACAGAGTCCAA
GACAACGTTCAAAACGTGCTGCAAAGGAAGATTAAGAAACGAATTTTTAAAGAGTTGTTA
ATTTCATCCCCTCTATGAGATTCATACCTATGAGCAAGTCAAGCTTCTCTAGAAATCCAA
TAAAACACATAAACCACATAAATTTTAATAGAACAACTTAAAAATTCATCGTAATACTTA
CCCTATGTTGTCTTCAAATCATTATGCATGGAGCATAATTAAAACTTTTTTTTTGATCTT
GCAATAGTTGATTCATAGAGTATAAGTGTTTTGCGTTTAAGATTCCAATTCTTATCTTTT
TGTTGCAAGATCACACCAATCATTATCATTTTATAATTGAAAAGAAAAAGAGTAAAAAGA
GATCATCAATGATGTTTGTT
>g12710.t16 Gene=g12710 Length=168
MDFTYYIQNFSALAYNREVKSESEATVSYSFLPSEQFAGRPFGLNIAISYRDSTGAGFME
AVFNETVLITELDEGLDGETFFLYVFFAAIFVLLLVVGQQFLGSIGKKKRSQNIRKQVET
GTSNNTDIDYEWLPAQTIRNLQNSPNGKGKISPKQSPRQRSKRAAKED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12710.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 168 | - |
| 6 | g12710.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 154 | - |
| 2 | g12710.t16 | PANTHER | PTHR12924:SF0 | TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT ALPHA | 1 | 161 | 5.8E-43 |
| 3 | g12710.t16 | PANTHER | PTHR12924 | TRANSLOCON-ASSOCIATED PROTEIN, ALPHA SUBUNIT | 1 | 161 | 5.8E-43 |
| 1 | g12710.t16 | Pfam | PF03896 | Translocon-associated protein (TRAP), alpha subunit | 1 | 167 | 2.5E-75 |
| 8 | g12710.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 80 | - |
| 9 | g12710.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 102 | - |
| 7 | g12710.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 103 | 168 | - |
| 4 | g12710.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 103 | - |
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:0005789 | endoplasmic reticulum membrane | CC |
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.
