General information for g12275.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1.
Parent gene
- The parent gene g12275 is located on chr_1: 22114543..22115579 (- 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 | g12275 | g12275.t1 | TTS | g12275.t1 | 22113841 | 22113841 |
| chr_1 | g12275 | g12275.t1 | isoform | g12275.t1 | 22114133 | 22115579 |
| chr_1 | g12275 | g12275.t1 | exon | g12275.t1.exon1 | 22114133 | 22114938 |
| chr_1 | g12275 | g12275.t1 | cds | g12275.t1.CDS1 | 22114133 | 22114938 |
| chr_1 | g12275 | g12275.t1 | exon | g12275.t1.exon2 | 22115009 | 22115579 |
| chr_1 | g12275 | g12275.t1 | cds | g12275.t1.CDS2 | 22115009 | 22115579 |
| chr_1 | g12275 | g12275.t1 | TSS | g12275.t1 | 22115633 | 22115633 |
Sequences
>g12275.t1 Gene=g12275 Length=1377
ATGAATTTTAAATCAAGTATTACAATATTTCTAGTGTTTCTAATTAGTTTAACTTCTTGT
AATTCAATTGATCAAGAAGTAGAAAATAAAAACGTAGACAGAACGATTGATATAACATCA
CAATTGGTAAAAATTACATACAAGATTACACTTGAGCACAAGTCTAAGAAACCGATTACA
AATTATGTATTTGTACTTCCCATCAATGAATGCAACAAAGTATCAATTGTTACTGCTCGT
GATGCTGCTAAGAAGGAACTCAAATTGACAACATCAAAGAATTCGGAAGAATGCGCATAC
ACGATGACGTTGTCTGCTGGAAGTAATCCAGTAATTTATGTTGAAGCTGTATTTTCAAAA
GCTCTTGAGCCATATCCAGTTGCTATTCCACAATCAGAACGTCAATTGGTTCGCTACTTT
GGAAGTGCATATTTCTATTCGCCATATAAAACTTTGTCTCAAAAGACCACAATTCATCTT
GCATCAAAAAGCGTTGAGAGTTATACTCAACTTAAACCATCATCGCAAAATGATGCTCAA
ATTTTCTATGGCCCTTATGAAAACATTGCACCAAATACAAAGCATGAAATAGTTGTTCAT
TACGAAAATAACACACCATTTATGACAATTACAAGATTAGAGCGCACAATTGAAATCTCA
CTTTGGGGCAATGTTGCTGTTGAAGAAACAATTGATATCATTCATTCTGGCGCTTTGCTT
AAAGGTTCATTCTCTCGATATGATTATCAAAAAGATTCTCGAAGTGGACCAGCAAGTGTA
AAATCATACAAAACAATTCTACCAGCATCAGCAACTGGTGTATATTATCGCGATATTAAT
GGAAATATTTCAACATCGGCGATGAGAATTTTAAAGGATTCAGTTGAACTTGATTTGAGA
CCACGTTTCCCTCTCTTTGGTGGTTGGCGTACACATTATACTGTTGGTTACAATGTTCCA
AGCTTTGAATATTTATTCCAAAGTGGAGATAATTACATGTTGAAAATGAGAGTTTTAGAT
CACGTTTTTGATGATATGATTGTTGATGAACTCATTACAAAAGTTATTCTGCCTGAAGGA
AGCAAAAATATTAAGCTTGTTACACCATATACAGTAGAACGCAAGCCTGATTCACTTCAT
TTTACTTATTTGGATATCACAGGACGTCCAGTCATTACATTCCGCAAAACTAATTTAGTT
GAGAATCATATCAACGATTTCAATCTTAAGTTCAATTTTTCACGCATCATGATGCTTCAA
GAACCATTGCTAGTCGTTGTGTTCTTTTATCTCATCTTTTTATTTGTAATCATTTGGACA
CGACTTGATTTCTCAATCATCAAGGAACGCGAGTCGCAACATTTGCATAAAGACTAA
>g12275.t1 Gene=g12275 Length=458
MNFKSSITIFLVFLISLTSCNSIDQEVENKNVDRTIDITSQLVKITYKITLEHKSKKPIT
NYVFVLPINECNKVSIVTARDAAKKELKLTTSKNSEECAYTMTLSAGSNPVIYVEAVFSK
ALEPYPVAIPQSERQLVRYFGSAYFYSPYKTLSQKTTIHLASKSVESYTQLKPSSQNDAQ
IFYGPYENIAPNTKHEIVVHYENNTPFMTITRLERTIEISLWGNVAVEETIDIIHSGALL
KGSFSRYDYQKDSRSGPASVKSYKTILPASATGVYYRDINGNISTSAMRILKDSVELDLR
PRFPLFGGWRTHYTVGYNVPSFEYLFQSGDNYMLKMRVLDHVFDDMIVDELITKVILPEG
SKNIKLVTPYTVERKPDSLHFTYLDITGRPVITFRKTNLVENHINDFNLKFNFSRIMMLQ
EPLLVVVFFYLIFLFVIIWTRLDFSIIKERESQHLHKD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12275.t1 | PANTHER | PTHR21049:SF0 | DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE SUBUNIT 1 | 8 | 452 | 1.9E-167 |
| 3 | g12275.t1 | PANTHER | PTHR21049 | RIBOPHORIN I | 8 | 452 | 1.9E-167 |
| 1 | g12275.t1 | Pfam | PF04597 | Ribophorin I | 28 | 438 | 9.0E-132 |
| 10 | g12275.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 11 | g12275.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 12 | g12275.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 17 | - |
| 14 | g12275.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 22 | - |
| 9 | g12275.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 422 | - |
| 13 | g12275.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 423 | 442 | - |
| 8 | g12275.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 443 | 458 | - |
| 7 | g12275.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 20 | 5.0 |
| 6 | g12275.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 5 | g12275.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
| 4 | g12275.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 417 | 439 | - |
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:0006486 | protein glycosylation | BP |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K12666 (oligosaccharyltransferase complex subunit alpha (ribophorin I))
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.
