General information for g7011.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 2.
Parent gene
- The parent gene g7011 is located on chr_2: 20628085..20628282 (- 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_2 | g7011 | g7011.t1 | TTS | g7011.t1 | 20625823 | 20625823 |
| chr_2 | g7011 | g7011.t1 | isoform | g7011.t1 | 20626125 | 20628282 |
| chr_2 | g7011 | g7011.t1 | exon | g7011.t1.exon1 | 20626125 | 20627786 |
| chr_2 | g7011 | g7011.t1 | cds | g7011.t1.CDS1 | 20626125 | 20627786 |
| chr_2 | g7011 | g7011.t1 | exon | g7011.t1.exon2 | 20627850 | 20628085 |
| chr_2 | g7011 | g7011.t1 | cds | g7011.t1.CDS2 | 20627850 | 20628085 |
| chr_2 | g7011 | g7011.t1 | exon | g7011.t1.exon3 | 20628270 | 20628282 |
| chr_2 | g7011 | g7011.t1 | cds | g7011.t1.CDS3 | 20628270 | 20628282 |
| chr_2 | g7011 | g7011.t1 | TSS | g7011.t1 | 20628359 | 20628359 |
Sequences
>g7011.t1 Gene=g7011 Length=1911
ATGAAGCGTTTAACATTAATATCCACTTTACTAGTCTTTGTGACTTGTGTTTATGCCACG
CGAACTGTTGATAACTTTTTGAGCAAATCAGATTTACAAAGACTGAATCAAATTTTTGCT
GATGGACTTCAATCTAGCGATCTACAAACACTTTATTATTCGGTCATTAATTCTAAGAAT
GTTCCTGCTGATATAAAATCAAATTTGTGCAAGAAACTCTCAGCTTTACATTCTGAATCA
AAATTAAATGATTTTGAAAAGAACTATTATTATACTGGAATTAGTACAACATTAGCATGC
AGCGAAAAAATTCCATCAGAACTTGTTAGTCAAATTAAAGCTTCGTTTAATAAAGATTTC
GCGTCTACACAAGAAATGTTTTATGCCTATTATACTCAAAAGTTTCTTGATCCAGCAGTT
GTGAAAGAAGACGCAACAAAAGAAACATTGGCTAAAAAATTACTGGTTTTATTGAAAAAA
GACGATTCTTTACAATCACTTGGTTATGGCTTTTATATTGCTGGAAACTTAGGACCAACT
GCAAGCTCGGTTGCTGATCGTGTTGAAGATGCAATTGCTCAAGCTGATGAAGTTGATGGA
AAATTGCTTCAATTTGAGGGTGGATTAAGTATTACTTCTTTGATCATAAATGGAGCATTA
AGAGTTACATCATTCAATAACAAACCAGCACCATTAACTGTTGAGCAAGCTAAAAAATTC
ACTTCATATTTCCTTTCAAGAAAATCGGTTACTCAAGCAAAAGGAGCTAGTTTGCTTTTG
GAGTCTCTTCGTTATATTATTAATGAAAAGAAAATTTCACCAGCTGCTATTCGAGTCGCT
GATAATGGTCAGTTGCCACCAGAGGATCCAGTTTTACGTATTCGTATTTGTGATTTATTC
GGTGAACCATTAGAAAAGAAGCCAGCATCAGTTAAAGTAACCTTCACATCAAAGAGTGAT
AACAAAAAAGTTCTTGAAGCTGAAAGTATGGTGCCATCTGCTTCTGATGCAACAGTTTAC
AAATTTGATCTGAAAGGAAAGAAATTGCAAAAAGGAACTTACAAAGTTGAAATTGATGCC
ACCACATACAAACAATCTAATTTGCTTGTGAATATCTTAGGCAAAGTTAAATTAGATAAA
ATTGATGTTTCTATCTCGGAAGCTGATTCGCAAACACCTTCAAAGAAAGTTTGGCTTGAT
AAAAACAGTAAATTCCCAGAGGTTTTCTTGTTAGATCATCAACAGAAATTCGGTCTTCGT
TTCGACTTGTTAGATGAACAGACTAATGGAATTTTGACTGTACATCAAGCTTTTGTTCGT
TTTTCTGATGCATCTGGAGATGAAATAATTTTTATTGCTGAACAAGATGTTGTTAAAGCT
TACAAATTCGAATTAGATGTTGGTGCAAGAGCTGGTGATTTTGCTGGCAAATCTGGAATT
TATAATGTTGATTTGATTATTGGAGACTCATCAATCGTCAATTCATTTGTGCGAAATCTT
GGCCAAGTCAACTTGAAATTCTCACTTGAAAGTAAAAAAGAATCTTCAACAACACCTAAA
CGTCAAGCACGTCCAGAAATTCACCATTTGTTCCGTGAACCAGAAAAACGACCACCACGT
TTTGTATCAGATTTATTCACCGGTTTGTGTTTGATACCAATTCTGATTCTCTTAATCTTA
TGGGGTCGCATCGGAATCAATACGTCTAACTTTAGCTTCAGTTTAAGTGCTTTAGGTTTT
CACGGAGGTCTTGGAGCAATTTTTTCATTATTCCTCTGCTTTTGGCTAAAATTAAATATG
TTCCAAACAATTCAGTATTTATTGGGACTTTCTATCATTACTTTCCTTTGTGGAAATAGA
GTACTAAGATATATTGCCAGTAAACGCTTAGAGAAATCAGAGAAGAACTAA
>g7011.t1 Gene=g7011 Length=636
MKRLTLISTLLVFVTCVYATRTVDNFLSKSDLQRLNQIFADGLQSSDLQTLYYSVINSKN
VPADIKSNLCKKLSALHSESKLNDFEKNYYYTGISTTLACSEKIPSELVSQIKASFNKDF
ASTQEMFYAYYTQKFLDPAVVKEDATKETLAKKLLVLLKKDDSLQSLGYGFYIAGNLGPT
ASSVADRVEDAIAQADEVDGKLLQFEGGLSITSLIINGALRVTSFNNKPAPLTVEQAKKF
TSYFLSRKSVTQAKGASLLLESLRYIINEKKISPAAIRVADNGQLPPEDPVLRIRICDLF
GEPLEKKPASVKVTFTSKSDNKKVLEAESMVPSASDATVYKFDLKGKKLQKGTYKVEIDA
TTYKQSNLLVNILGKVKLDKIDVSISEADSQTPSKKVWLDKNSKFPEVFLLDHQQKFGLR
FDLLDEQTNGILTVHQAFVRFSDASGDEIIFIAEQDVVKAYKFELDVGARAGDFAGKSGI
YNVDLIIGDSSIVNSFVRNLGQVNLKFSLESKKESSTTPKRQARPEIHHLFREPEKRPPR
FVSDLFTGLCLIPILILLILWGRIGINTSNFSFSLSALGFHGGLGAIFSLFLCFWLKLNM
FQTIQYLLGLSIITFLCGNRVLRYIASKRLEKSEKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g7011.t1 | PANTHER | PTHR12640:SF0 | DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE SUBUNIT 2 | 11 | 632 | 3.6E-126 |
| 4 | g7011.t1 | PANTHER | PTHR12640 | RIBOPHORIN II | 11 | 632 | 3.6E-126 |
| 2 | g7011.t1 | Pfam | PF05817 | Oligosaccharyltransferase subunit Ribophorin II | 9 | 628 | 1.2E-184 |
| 14 | g7011.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 15 | g7011.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 16 | g7011.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 20 | g7011.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 13 | g7011.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 540 | - |
| 19 | g7011.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 541 | 561 | - |
| 11 | g7011.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 562 | 572 | - |
| 17 | g7011.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 573 | 598 | - |
| 12 | g7011.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 599 | 603 | - |
| 18 | g7011.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 604 | 622 | - |
| 10 | g7011.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 623 | 636 | - |
| 9 | g7011.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 1 | g7011.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 8 | g7011.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 6 | g7011.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 545 | 567 | - |
| 7 | g7011.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 574 | 596 | - |
| 5 | g7011.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 600 | 622 | - |
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:0008250 | oligosaccharyltransferase complex | CC |
| GO:0016021 | integral component of membrane | CC |
| GO:0006487 | protein N-linked glycosylation | BP |
KEGG
Orthology
- This transcript has been annotated with K12667 (oligosaccharyltransferase complex subunit delta (ribophorin II))
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.
