General information for g11870.t3
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.t3 | TSS | g11870.t3 | 18863175 | 18863175 |
| chr_1 | g11870 | g11870.t3 | isoform | g11870.t3 | 18863329 | 18864790 |
| chr_1 | g11870 | g11870.t3 | exon | g11870.t3.exon1 | 18863329 | 18863964 |
| chr_1 | g11870 | g11870.t3 | cds | g11870.t3.CDS1 | 18863404 | 18863964 |
| chr_1 | g11870 | g11870.t3 | exon | g11870.t3.exon2 | 18864030 | 18864311 |
| chr_1 | g11870 | g11870.t3 | cds | g11870.t3.CDS2 | 18864030 | 18864311 |
| chr_1 | g11870 | g11870.t3 | exon | g11870.t3.exon3 | 18864377 | 18864790 |
| chr_1 | g11870 | g11870.t3 | cds | g11870.t3.CDS3 | 18864377 | 18864790 |
| chr_1 | g11870 | g11870.t3 | TTS | g11870.t3 | 18865384 | 18865384 |
Sequences
>g11870.t3 Gene=g11870 Length=1332
GTCTTCTCATTGGATTCACCGGACACATTTCAATGTAGCTATTCGCCAAGCTTGAGGTCC
GCTCGAGTTGGCAACATGGAGCGTATCGCCGAACAGGTCGCTACGCTTTGTTCCACTTTG
GGCGAGTATCCTTCTATACGTTATCGCAGTGATTGGGAGCGTAATGTTGAATTGGCCCAA
TTGATACAACAAAAATTGGACGCCTACAAAGCCGATGAACCAACAATGGGTGAAGGACCA
GAAAAGGCCAAATCAACATTGTTGATTCTGGATCGTGGCTTTGATTGCGTTTCTCCATTA
CTGCATGAATTAACGTTACAAGCAATGGCATATGATTTGCTACCAATTTCAAATGATGTC
TACAAGTATGAAAATCAAGGCGCAGAGAAGGAAGTCTTATTGGATGAGAATGATGAATTG
TGGTGTGAATTGCGTCATCAACATATTGCAGTTGTTTCTCAAAAGGTTACCGCTAATTTG
AAGAATTTTACCGAATCTAAGCGCATGTCTTCAACTGATAAAGCATCAATGAGAGATCTC
TCGCAAATGATTAAAAAAATGCCGCAGTATCAAAAAGAACTCTCAAAATATGCAACACAT
TTGCATTTGGCCGAAGATTGTATGAAAGCTTATCAAGGTTACATTGATAAATTATGTCGG
GTTGAACAAGATTTGGCTATGGGAACAGATGCTGAAGGAGAAAAGATCAAAGATCATATG
CGTAATATTGTTCCAATTCTCTTAGATACATCTGTTTCTAATTACGATAAAGTACGCATC
ATTGCACTTTATGTGATGATTAAAAATGGCATTTCTGAAGAAAATTTTACAAAATTAGCA
ACACATGCAGGAATTGAACAACGTGAACGTGAAATGATTTTAAATTTAAGCCATTTGGGT
ATTAATGTAATTTCAGATGGAAGTCGTCGAAAGCAATATCAAATTCCTCGTAAAGAAAGA
ATCACAGAGCAAACGTATCAAATGTCTCGCTGGACACCAGTTATAAAAGATCTCATGGAA
GATTGTATTGATGAGAAATTGGATCAAAAACATTTTCCATTCTTGGCAAATCGCTCGGGT
CAAACATCTTATAGTGTTCCAACAAGCGCTCGTTATGGTCATTGGCACAAAGATAAATCA
CAGGCTCCTGTTATCCGAAATGTACCACGTCTTATTGTCTTCATAGTTGGTGGAATGAGT
TATTCAGAAATGCGATGTGCATATGAAGTTACAAACGCTTATAAAAATTGGGAAGTAATA
ATTGGATCTTCACACATTTTAACTCCTGAAGGCTTTTTAAGTGATTTGGGTGCAATTTCA
AAGGATGATTAA
>g11870.t3 Gene=g11870 Length=418
MERIAEQVATLCSTLGEYPSIRYRSDWERNVELAQLIQQKLDAYKADEPTMGEGPEKAKS
TLLILDRGFDCVSPLLHELTLQAMAYDLLPISNDVYKYENQGAEKEVLLDENDELWCELR
HQHIAVVSQKVTANLKNFTESKRMSSTDKASMRDLSQMIKKMPQYQKELSKYATHLHLAE
DCMKAYQGYIDKLCRVEQDLAMGTDAEGEKIKDHMRNIVPILLDTSVSNYDKVRIIALYV
MIKNGISEENFTKLATHAGIEQREREMILNLSHLGINVISDGSRRKQYQIPRKERITEQT
YQMSRWTPVIKDLMEDCIDEKLDQKHFPFLANRSGQTSYSVPTSARYGHWHKDKSQAPVI
RNVPRLIVFIVGGMSYSEMRCAYEVTNAYKNWEVIIGSSHILTPEGFLSDLGAISKDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11870.t3 | Coils | Coil | Coil | 416 | 418 | - |
| 6 | g11870.t3 | Gene3D | G3DSA:3.40.50.1910 | - | 1 | 411 | 6.1E-153 |
| 7 | g11870.t3 | Gene3D | G3DSA:3.90.830.10 | Syntaxin Binding Protein 1; Chain A | 78 | 187 | 6.1E-153 |
| 5 | g11870.t3 | Gene3D | G3DSA:1.25.40.60 | - | 188 | 307 | 6.1E-153 |
| 2 | g11870.t3 | PANTHER | PTHR11679:SF35 | SYNTAXIN-BINDING PROTEIN 1 | 1 | 412 | 4.2E-194 |
| 3 | g11870.t3 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 1 | 412 | 4.2E-194 |
| 1 | g11870.t3 | Pfam | PF00995 | Sec1 family | 1 | 410 | 1.7E-88 |
| 4 | g11870.t3 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 1 | 416 | 1.03E-130 |
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.
