General information for g11870.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein ROP.
Parent gene
- The parent gene g11870 is located on chr_1: 18864377..18866103 (+ 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 | g11870 | g11870.t2 | TSS | g11870.t2 | 18860436 | 18860436 |
| chr_1 | g11870 | g11870.t2 | isoform | g11870.t2 | 18860526 | 18863964 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon1 | 18860526 | 18860553 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS1 | 18860526 | 18860553 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon2 | 18860955 | 18861119 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS2 | 18860955 | 18861119 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon3 | 18861194 | 18861263 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS3 | 18861194 | 18861263 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon4 | 18861327 | 18861412 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS4 | 18861327 | 18861412 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon5 | 18861853 | 18861956 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS5 | 18861853 | 18861956 |
| chr_1 | g11870 | g11870.t2 | exon | g11870.t2.exon6 | 18863329 | 18863964 |
| chr_1 | g11870 | g11870.t2 | cds | g11870.t2.CDS6 | 18863329 | 18863964 |
| chr_1 | g11870 | g11870.t2 | TTS | g11870.t2 | NA | NA |
Sequences
>g11870.t2 Gene=g11870 Length=1089
ATGGCTTTAAAAGTGCTCGTTGGTCAAAAAATTATGAATGAAGTCATCAAATATAAAGGA
CCTGCAAAAAAATCGCAGCCTGGTCAAAAATCATCAAATGTGGAATGGCGTGTCTTGGTT
GTTGATAAACTTTCAATGCGAATGGTCTCAGCCTGTACTAAAATGCACGACCTTTCAGCT
GAGGCAATAACATTGGTTGAAGATATTAACAAGAAACGCGAACCGTTACAAACAATGGAA
GCAGTATATTTGATAACACCCTGTGAAGAGTCAGTGCGGGGATTAATTCGAGATTTTGAG
TCACCCACTCGTCCACTTTATAAAGCAGCTCATGTTTTCTTCACAGAAGTGTGTCCTGAT
GAAATGTTTAATGATATTTGCAAATCAATGGCAGCACGTAGAATTAAAACTTTAAAAGAA
ATCAACATTGCATTTCTTCCATACGAATGTCAGGTCTTCTCATTGGATTCACCGGACACA
TTTCAATGTAGCTATTCGCCAAGCTTGAGGTCCGCTCGAGTTGGCAACATGGAGCGTATC
GCCGAACAGGTCGCTACGCTTTGTTCCACTTTGGGCGAGTATCCTTCTATACGTTATCGC
AGTGATTGGGAGCGTAATGTTGAATTGGCCCAATTGATACAACAAAAATTGGACGCCTAC
AAAGCCGATGAACCAACAATGGGTGAAGGACCAGAAAAGGCCAAATCAACATTGTTGATT
CTGGATCGTGGCTTTGATTGCGTTTCTCCATTACTGCATGAATTAACGTTACAAGCAATG
GCATATGATTTGCTACCAATTTCAAATGATGTCTACAAGTATGAAAATCAAGGCGCAGAG
AAGGAAGTCTTATTGGATGAGAATGATGAATTGTGGTGTGAATTGCGTCATCAACATATT
GCAGTTGTTTCTCAAAAGGTTACCGCTAATTTGAAGAATTTTACCGAATCTAAGCGCATG
TCTTCAACTGATAAAGCATCAATGAGAGATCTCTCGCAAATGATTAAAAAAATGCCGCAG
TATCAAAAAGAACTCTCAAAATATGCAACACATTTGCATTTGGCCGAAGATTGTATGAAA
GCTTATCAA
>g11870.t2 Gene=g11870 Length=363
MALKVLVGQKIMNEVIKYKGPAKKSQPGQKSSNVEWRVLVVDKLSMRMVSACTKMHDLSA
EAITLVEDINKKREPLQTMEAVYLITPCEESVRGLIRDFESPTRPLYKAAHVFFTEVCPD
EMFNDICKSMAARRIKTLKEINIAFLPYECQVFSLDSPDTFQCSYSPSLRSARVGNMERI
AEQVATLCSTLGEYPSIRYRSDWERNVELAQLIQQKLDAYKADEPTMGEGPEKAKSTLLI
LDRGFDCVSPLLHELTLQAMAYDLLPISNDVYKYENQGAEKEVLLDENDELWCELRHQHI
AVVSQKVTANLKNFTESKRMSSTDKASMRDLSQMIKKMPQYQKELSKYATHLHLAEDCMK
AYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11870.t2 | Gene3D | G3DSA:3.40.50.2060 | - | 1 | 140 | 0 |
| 5 | g11870.t2 | Gene3D | G3DSA:3.40.50.1910 | - | 145 | 258 | 0 |
| 7 | g11870.t2 | Gene3D | G3DSA:3.90.830.10 | Syntaxin Binding Protein 1; Chain A | 259 | 363 | 0 |
| 2 | g11870.t2 | PANTHER | PTHR11679:SF62 | SI:RP71-10D23.3 | 7 | 363 | 0 |
| 3 | g11870.t2 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 7 | 363 | 0 |
| 1 | g11870.t2 | Pfam | PF00995 | Sec1 family | 37 | 362 | 0 |
| 4 | g11870.t2 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 9 | 363 | 0 |
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:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
