General information for g6650.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Translocation protein SEC62.
Parent gene
- The parent gene g6650 is located on chr_2: 17942779..17944049 (- 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 | g6650 | g6650.t3 | TTS | g6650.t3 | 17941016 | 17941016 |
| chr_2 | g6650 | g6650.t3 | isoform | g6650.t3 | 17941126 | 17942123 |
| chr_2 | g6650 | g6650.t3 | exon | g6650.t3.exon1 | 17941126 | 17941202 |
| chr_2 | g6650 | g6650.t3 | cds | g6650.t3.CDS1 | 17941155 | 17941202 |
| chr_2 | g6650 | g6650.t3 | exon | g6650.t3.exon2 | 17941271 | 17941504 |
| chr_2 | g6650 | g6650.t3 | cds | g6650.t3.CDS2 | 17941271 | 17941504 |
| chr_2 | g6650 | g6650.t3 | exon | g6650.t3.exon3 | 17941582 | 17942123 |
| chr_2 | g6650 | g6650.t3 | cds | g6650.t3.CDS3 | 17941582 | 17942115 |
| chr_2 | g6650 | g6650.t3 | TSS | g6650.t3 | 17942573 | 17942573 |
Sequences
>g6650.t3 Gene=g6650 Length=853
TTGATTATATGGATAAAATGCTTGCACATAAATTTTTTCATCGTGCAAAAAAGATACCTG
TTAGTGAGATGGAATTGAGAGGTGGACGCACAAAAGACAAATCAAAAGATCAAGAGAAAA
AAGAAACAGATGCTGAAAGCTCACATGAGAAAGACAAAAGCGATAAAGCAACATCAGAAA
AGAAAAAAAGGAAAATTCGCTTGGAAATGCATCCACAACAGATTTTTATCGATGGACATG
AAGCATATGTCTGGATTTATGATCCTATTCCGATGACTTATTGGATCTTTGGAGCTCTTG
TTGTAATTGGAGCAATAGTCATCTGTTTATTCCCACTCTGGCCACCACAATTGCGAACTG
GCGTCTACTATCTATCAATGACAGCAGCTGGATTTTTAGTCTTTCTTTTAGCTCTCGTGG
TAGTAAGGTTCATACTATTTTGCACTATATGGATATGTACTGGCGGCAAGCATCACTTCT
GGTTCCTTCTTAATCTCACTGAAGATGTAGGTTTTATTGATTCATTTAAACCACTCTATA
AGCATGACTATATTGACAGTTCTGATACTAAAAATAAAAAAGATAAGGACAAAAAGAAAA
AGAAGAAGAAGGACAGTGATGACGAGAGTGGTAATAATAAGGAATCTGAATTGGTCGATA
CAAAAGCTAAGGAGAGTGAAACAAATAATGAGGGCTCTATTTTGCAAAGGAGAAAAACAA
AAGCAAAAGAGCAAAATGAAGATATAATCAAAGATAATGAAGAAAGAAAAAAGTATAAAG
CTCCGACTCACAAAGGTCATCAACTGATAAAGATTTTGAAATAGTGGATGCAGAAGAAGA
CCATGAAGAATAA
>g6650.t3 Gene=g6650 Length=271
MDKMLAHKFFHRAKKIPVSEMELRGGRTKDKSKDQEKKETDAESSHEKDKSDKATSEKKK
RKIRLEMHPQQIFIDGHEAYVWIYDPIPMTYWIFGALVVIGAIVICLFPLWPPQLRTGVY
YLSMTAAGFLVFLLALVVVRFILFCTIWICTGGKHHFWFLLNLTEDVGFIDSFKPLYKHD
YIDSSDTKNKKDKDKKKKKKKDSDDESGNNKESELVDTKAKESETNNEGSILQRRKTKAK
EQNEDIIKDNEERKKYKAPTHKGHQLIKILK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6650.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 61 | - |
| 8 | g6650.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 188 | 271 | - |
| 7 | g6650.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 258 | - |
| 2 | g6650.t3 | PANTHER | PTHR12443:SF9 | TRANSLOCATION PROTEIN SEC62 | 1 | 254 | 1.4E-68 |
| 3 | g6650.t3 | PANTHER | PTHR12443 | TRANSLOCATION PROTEIN SEC62 | 1 | 254 | 1.4E-68 |
| 1 | g6650.t3 | Pfam | PF03839 | Translocation protein Sec62 | 7 | 200 | 1.7E-67 |
| 10 | g6650.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 90 | - |
| 12 | g6650.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 112 | - |
| 11 | g6650.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 113 | 117 | - |
| 13 | g6650.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 118 | 150 | - |
| 9 | g6650.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 151 | 271 | - |
| 5 | g6650.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 112 | - |
| 4 | g6650.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 122 | 144 | - |
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:0030176 | integral component of endoplasmic reticulum membrane | CC |
| GO:0015031 | protein transport | BP |
KEGG
Orthology
- This transcript has been annotated with K12275 (translocation protein SEC62)
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.
