General information for g12710.t20
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.t20 | TTS | g12710.t20 | 25414039 | 25414039 |
| chr_1 | g12710 | g12710.t20 | isoform | g12710.t20 | 25414098 | 25415531 |
| chr_1 | g12710 | g12710.t20 | exon | g12710.t20.exon1 | 25414098 | 25415043 |
| chr_1 | g12710 | g12710.t20 | cds | g12710.t20.CDS1 | 25414443 | 25415043 |
| chr_1 | g12710 | g12710.t20 | exon | g12710.t20.exon2 | 25415101 | 25415329 |
| chr_1 | g12710 | g12710.t20 | cds | g12710.t20.CDS2 | 25415101 | 25415329 |
| chr_1 | g12710 | g12710.t20 | exon | g12710.t20.exon3 | 25415471 | 25415531 |
| chr_1 | g12710 | g12710.t20 | cds | g12710.t20.CDS3 | 25415471 | 25415531 |
| chr_1 | g12710 | g12710.t20 | TSS | g12710.t20 | 25415638 | 25415638 |
Sequences
>g12710.t20 Gene=g12710 Length=1236
ATGAAGCATTCATTGCTATTAGTTCTTCTCATTTTACCTGCATTTCTATTTATTTTTGAT
GACTCTTATATAGGCAGCAAAGTGTTTGTTAGAGCAAATGAAGACGAAATTGATGAGGAT
TTAGTTGATGTCGAAAATGAAGGTGATGCAGATGAAGCAAGTGAAAGTGCGCTGACTGGC
GATGATGTGGAGGCAGATGAGACTGGTGAAAGTACGAAATCTCCTGATGCTGACACTCAA
TTGCTCTTTGTTCGACCACTTTATACACCAGGATCACAACTTGAATTACCTGGCGGTGTT
CCAGTAGAGTTCTTAATTGGCTTCTTAAATAAAGGCAAAAATGATTTCATTATTGAGAGT
GTTGAAGCTTCATTCCGTTATCCAATGGATTTCACTTACTACATTCAAAATTTCTCAGCA
CTTGCATATAACCGTGAAGTTAAATCAGAGAGTGAAGCAACTGTATCATACTCATTCCTT
CCATCAGAACAATTTGCTGGTCGTCCTTTTGGTTTGAATATTGCCATTAGTTATCGTGAT
TCAACTGGTGCAGGTTTTATGGAAGCAGTTTTCAATGAAACTGTTCTCATCACAGAATTA
GATGAAGGTCTTGATGGCGAAACATTCTTTTTATATGTGTTCTTTGCAGCTATTTTTGTT
TTACTTCTTGTTGTTGGACAACAATTCCTCGGTTCAATTGGCAAGAAGAAACGTTCACAA
AACATTCGTAAGCAAGTTGAGACTGGTACATCAAATAACACCGATATTGATTATGAATGG
CTTCCTGCTCAAACAATTAGAAATTTACAAAATTCACCAAATGGCAAAGGAAAAATCTCG
CCAAAACAGAGTCCAAGACAACGTTCAAAACGTGCTGCAAAGGAAGATTAAGAAACGAAT
TTTTAAAGAGTTGTTAATTTCATCCCCTCTATGAGATTCATACCTATGAGCAAGTCAAGC
TTCTCTAGAAATCCAATAAAACACATAAACCACATAAATTTTAATAGAACAACTTAAAAA
TTCATCGTAATACTTACCCTATGTTGTCTTCAAATCATTATGCATGGAGCATAATTAAAA
CTTTTTTTTTGATCTTGCAATAGTTGATTCATAGAGTATAAGTGTTTTGCGTTTAAGATT
CCAATTCTTATCTTTTTGTTGCAAGATCACACCAATCATTATCATTTTATAATTGAAAAG
AAAAAGAGTAAAAAGAGATCATCAATGATGTTTGTT
>g12710.t20 Gene=g12710 Length=296
MKHSLLLVLLILPAFLFIFDDSYIGSKVFVRANEDEIDEDLVDVENEGDADEASESALTG
DDVEADETGESTKSPDADTQLLFVRPLYTPGSQLELPGGVPVEFLIGFLNKGKNDFIIES
VEASFRYPMDFTYYIQNFSALAYNREVKSESEATVSYSFLPSEQFAGRPFGLNIAISYRD
STGAGFMEAVFNETVLITELDEGLDGETFFLYVFFAAIFVLLLVVGQQFLGSIGKKKRSQ
NIRKQVETGTSNNTDIDYEWLPAQTIRNLQNSPNGKGKISPKQSPRQRSKRAAKED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12710.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 75 | - |
| 7 | g12710.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 65 | - |
| 8 | g12710.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 296 | - |
| 9 | g12710.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 282 | - |
| 2 | g12710.t20 | PANTHER | PTHR12924:SF0 | TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT ALPHA | 4 | 289 | 2.8E-69 |
| 3 | g12710.t20 | PANTHER | PTHR12924 | TRANSLOCON-ASSOCIATED PROTEIN, ALPHA SUBUNIT | 4 | 289 | 2.8E-69 |
| 1 | g12710.t20 | Pfam | PF03896 | Translocon-associated protein (TRAP), alpha subunit | 5 | 295 | 7.3E-114 |
| 13 | g12710.t20 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 14 | g12710.t20 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g12710.t20 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 17 | g12710.t20 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 16 | - |
| 12 | g12710.t20 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 208 | - |
| 16 | g12710.t20 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 230 | - |
| 11 | g12710.t20 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 231 | 296 | - |
| 10 | g12710.t20 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 4 | g12710.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 24 | - |
| 5 | g12710.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
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 transcript has been annotated with K13249 (translocon-associated protein subunit alpha)
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.
