General information for g12710.t21
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.t21 | TTS | g12710.t21 | 25414039 | 25414039 |
| chr_1 | g12710 | g12710.t21 | isoform | g12710.t21 | 25414098 | 25415531 |
| chr_1 | g12710 | g12710.t21 | exon | g12710.t21.exon1 | 25414098 | 25415043 |
| chr_1 | g12710 | g12710.t21 | cds | g12710.t21.CDS1 | 25414443 | 25415043 |
| chr_1 | g12710 | g12710.t21 | exon | g12710.t21.exon2 | 25415101 | 25415313 |
| chr_1 | g12710 | g12710.t21 | cds | g12710.t21.CDS2 | 25415101 | 25415313 |
| chr_1 | g12710 | g12710.t21 | exon | g12710.t21.exon3 | 25415506 | 25415531 |
| chr_1 | g12710 | g12710.t21 | cds | g12710.t21.CDS3 | 25415506 | 25415531 |
| chr_1 | g12710 | g12710.t21 | TSS | g12710.t21 | 25415638 | 25415638 |
Sequences
>g12710.t21 Gene=g12710 Length=1185
ATGAAGCATTCATTGCTATTAGTTCTCAAAGTGTTTGTTAGAGCAAATGAAGACGAAATT
GATGAGGATTTAGTTGATGTCGAAAATGAAGGTGATGCAGATGAAGCAAGTGAAAGTGCG
CTGACTGGCGATGATGTGGAGGCAGATGAGACTGGTGAAAGTACGAAATCTCCTGATGCT
GACACTCAATTGCTCTTTGTTCGACCACTTTATACACCAGGATCACAACTTGAATTACCT
GGCGGTGTTCCAGTAGAGTTCTTAATTGGCTTCTTAAATAAAGGCAAAAATGATTTCATT
ATTGAGAGTGTTGAAGCTTCATTCCGTTATCCAATGGATTTCACTTACTACATTCAAAAT
TTCTCAGCACTTGCATATAACCGTGAAGTTAAATCAGAGAGTGAAGCAACTGTATCATAC
TCATTCCTTCCATCAGAACAATTTGCTGGTCGTCCTTTTGGTTTGAATATTGCCATTAGT
TATCGTGATTCAACTGGTGCAGGTTTTATGGAAGCAGTTTTCAATGAAACTGTTCTCATC
ACAGAATTAGATGAAGGTCTTGATGGCGAAACATTCTTTTTATATGTGTTCTTTGCAGCT
ATTTTTGTTTTACTTCTTGTTGTTGGACAACAATTCCTCGGTTCAATTGGCAAGAAGAAA
CGTTCACAAAACATTCGTAAGCAAGTTGAGACTGGTACATCAAATAACACCGATATTGAT
TATGAATGGCTTCCTGCTCAAACAATTAGAAATTTACAAAATTCACCAAATGGCAAAGGA
AAAATCTCGCCAAAACAGAGTCCAAGACAACGTTCAAAACGTGCTGCAAAGGAAGATTAA
GAAACGAATTTTTAAAGAGTTGTTAATTTCATCCCCTCTATGAGATTCATACCTATGAGC
AAGTCAAGCTTCTCTAGAAATCCAATAAAACACATAAACCACATAAATTTTAATAGAACA
ACTTAAAAATTCATCGTAATACTTACCCTATGTTGTCTTCAAATCATTATGCATGGAGCA
TAATTAAAACTTTTTTTTTGATCTTGCAATAGTTGATTCATAGAGTATAAGTGTTTTGCG
TTTAAGATTCCAATTCTTATCTTTTTGTTGCAAGATCACACCAATCATTATCATTTTATA
ATTGAAAAGAAAAAGAGTAAAAAGAGATCATCAATGATGTTTGTT
>g12710.t21 Gene=g12710 Length=279
MKHSLLLVLKVFVRANEDEIDEDLVDVENEGDADEASESALTGDDVEADETGESTKSPDA
DTQLLFVRPLYTPGSQLELPGGVPVEFLIGFLNKGKNDFIIESVEASFRYPMDFTYYIQN
FSALAYNREVKSESEATVSYSFLPSEQFAGRPFGLNIAISYRDSTGAGFMEAVFNETVLI
TELDEGLDGETFFLYVFFAAIFVLLLVVGQQFLGSIGKKKRSQNIRKQVETGTSNNTDID
YEWLPAQTIRNLQNSPNGKGKISPKQSPRQRSKRAAKED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12710.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 48 | - |
| 8 | g12710.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 59 | - |
| 6 | g12710.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 279 | - |
| 7 | g12710.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 265 | - |
| 2 | g12710.t21 | PANTHER | PTHR12924:SF0 | TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT ALPHA | 4 | 272 | 4.1E-68 |
| 3 | g12710.t21 | PANTHER | PTHR12924 | TRANSLOCON-ASSOCIATED PROTEIN, ALPHA SUBUNIT | 4 | 272 | 4.1E-68 |
| 1 | g12710.t21 | Pfam | PF03896 | Translocon-associated protein (TRAP), alpha subunit | 11 | 278 | 6.2E-111 |
| 12 | g12710.t21 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 13 | g12710.t21 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g12710.t21 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 16 | g12710.t21 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 15 | - |
| 11 | g12710.t21 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 191 | - |
| 15 | g12710.t21 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 192 | 213 | - |
| 10 | g12710.t21 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 214 | 279 | - |
| 9 | g12710.t21 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 15 | - |
| 4 | g12710.t21 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 195 | 217 | - |
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.
