General information for g6650.t11
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.t11 | TTS | g6650.t11 | 17941016 | 17941016 |
| chr_2 | g6650 | g6650.t11 | isoform | g6650.t11 | 17941126 | 17943095 |
| chr_2 | g6650 | g6650.t11 | exon | g6650.t11.exon1 | 17941126 | 17941213 |
| chr_2 | g6650 | g6650.t11 | cds | g6650.t11.CDS1 | 17941208 | 17941213 |
| chr_2 | g6650 | g6650.t11 | exon | g6650.t11.exon2 | 17941283 | 17941504 |
| chr_2 | g6650 | g6650.t11 | cds | g6650.t11.CDS2 | 17941283 | 17941504 |
| chr_2 | g6650 | g6650.t11 | exon | g6650.t11.exon3 | 17941582 | 17942334 |
| chr_2 | g6650 | g6650.t11 | cds | g6650.t11.CDS3 | 17941582 | 17942334 |
| chr_2 | g6650 | g6650.t11 | exon | g6650.t11.exon4 | 17943054 | 17943095 |
| chr_2 | g6650 | g6650.t11 | cds | g6650.t11.CDS4 | 17943054 | 17943095 |
| chr_2 | g6650 | g6650.t11 | TSS | g6650.t11 | 17943212 | 17943212 |
Sequences
>g6650.t11 Gene=g6650 Length=1105
ATGTCGGGAAAAGATAAAAGAGTCAATAAAAAGAAAAAAGATGAATATAAAGAGAATGAT
GACGAGCAGGAAAAGGCAAGTAAAGAAGAGTATAAAGTTGCCAAGTGGATACGCAACAAT
GTTCCCGTGAAAAAAACTAAATTTCTCAATCACAATGTTGAATATTTTACATCAGCAAAA
GCGCTTGATGCTCTGATGACATCAAAATTCGCCCAAGGTGATAATTGTCTTTTTCCAACA
CGTCAAATTGCAATTGATTATATGGATAAAATGCTTGCACATAAATTTTTTCATCGTGCA
AAAAAGATACCTGTTAGTGAGATGGAATTGAGAGGTGGACGCACAAAAGACAAATCAAAA
GATCAAGAGAAAAAAGAAACAGATGCTGAAAGCTCACATGAGAAAGACAAAAGCGATAAA
GCAACATCAGAAAAGAAAAAAAGGAAAATTCGCTTGGAAATGCATCCACAACAGATTTTT
ATCGATGGACATGAAGCATATGTCTGGATTTATGATCCTATTCCGATGACTTATTGGATC
TTTGGAGCTCTTGTTGTAATTGGAGCAATAGTCATCTGTTTATTCCCACTCTGGCCACCA
CAATTGCGAACTGGCGTCTACTATCTATCAATGACAGCAGCTGGATTTTTAGTCTTTCTT
TTAGCTCTCGTGGTAGTAAGGTTCATACTATTTTGCACTATATGGATATGTACTGGCGGC
AAGCATCACTTCTGGTTCCTTCTTAATCTCACTGAAGATGTAGGTTTTATTGATTCATTT
AAACCACTCTATAAGCATGACTATATTGACAGTTCTGATACTAAAAATAAAAAAGATAAG
GACAAAAAGAAAAAGAAGAAGAAGGACAGTGATGACGAGAGTGGTAATAATAAGGAATCT
GAATTGGTCGATACAAAAGCTAAGGAGAGTGAAACAAATAATGAGGGCTCTATTTTGCAA
AGGAGAAAAACAAAAGCAAAAGAGCAAAATGAAGATATAATCAAAGATAATGAAGAATTC
TGAGTCAGAAAGCTCCGACTCACAAAGGTCATCAACTGATAAAGATTTTGAAATAGTGGA
TGCAGAAGAAGACCATGAAGAATAA
>g6650.t11 Gene=g6650 Length=340
MSGKDKRVNKKKKDEYKENDDEQEKASKEEYKVAKWIRNNVPVKKTKFLNHNVEYFTSAK
ALDALMTSKFAQGDNCLFPTRQIAIDYMDKMLAHKFFHRAKKIPVSEMELRGGRTKDKSK
DQEKKETDAESSHEKDKSDKATSEKKKRKIRLEMHPQQIFIDGHEAYVWIYDPIPMTYWI
FGALVVIGAIVICLFPLWPPQLRTGVYYLSMTAAGFLVFLLALVVVRFILFCTIWICTGG
KHHFWFLLNLTEDVGFIDSFKPLYKHDYIDSSDTKNKKDKDKKKKKKKDSDDESGNNKES
ELVDTKAKESETNNEGSILQRRKTKAKEQNEDIIKDNEEF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6650.t11 | Coils | Coil | Coil | 9 | 29 | - |
| 9 | g6650.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 29 | - |
| 6 | g6650.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 148 | - |
| 7 | g6650.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 275 | 340 | - |
| 8 | g6650.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 285 | 340 | - |
| 2 | g6650.t11 | PANTHER | PTHR12443:SF9 | TRANSLOCATION PROTEIN SEC62 | 15 | 325 | 7.4E-88 |
| 3 | g6650.t11 | PANTHER | PTHR12443 | TRANSLOCATION PROTEIN SEC62 | 15 | 325 | 7.4E-88 |
| 1 | g6650.t11 | Pfam | PF03839 | Translocation protein Sec62 | 94 | 287 | 1.9E-67 |
| 11 | g6650.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 177 | - |
| 14 | g6650.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 178 | 199 | - |
| 13 | g6650.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 200 | 204 | - |
| 15 | g6650.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 237 | - |
| 12 | g6650.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 238 | 340 | - |
| 5 | g6650.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 177 | 199 | - |
| 4 | g6650.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 231 | - |
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. There were no conditions that were differentially expressed