General information for g11870.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | isoform | g11870.t4 | 18864377 | 18866103 |
| chr_1 | g11870 | g11870.t4 | exon | g11870.t4.exon1 | 18864377 | 18865522 |
| chr_1 | g11870 | g11870.t4 | cds | g11870.t4.CDS1 | 18864440 | 18864790 |
| chr_1 | g11870 | g11870.t4 | exon | g11870.t4.exon2 | 18865801 | 18866103 |
| chr_1 | g11870 | g11870.t4 | TTS | g11870.t4 | 18866421 | 18866421 |
| chr_1 | g11870 | g11870.t4 | TSS | g11870.t4 | NA | NA |
Sequences
>g11870.t4 Gene=g11870 Length=1449
GGAAGTCGTCGAAAGCAATATCAAATTCCTCGTAAAGAAAGAATCACAGAGCAAACGTAT
CAAATGTCTCGCTGGACACCAGTTATAAAAGATCTCATGGAAGATTGTATTGATGAGAAA
TTGGATCAAAAACATTTTCCATTCTTGGCAAATCGCTCGGGTCAAACATCTTATAGTGTT
CCAACAAGCGCTCGTTATGGTCATTGGCACAAAGATAAATCACAGGCTCCTGTTATCCGA
AATGTACCACGTCTTATTGTCTTCATAGTTGGTGGAATGAGTTATTCAGAAATGCGATGT
GCATATGAAGTTACAAACGCTTATAAAAATTGGGAAGTAATAATTGGATCTTCACACATT
TTAACTCCTGAAGGCTTTTTAAGTGATTTGGGTGCAATTTCAAAGGATGATTAAGTATAT
TTTAATTAGTAAAAAATAGTTTACTATCCTATATACTATGATAACAACTTTACTTACTTC
TTGGCTTATAAATGTGATTTTTCTCAATTTTCTAGAGAAGTAGGTATTTCTTTTTCAAAA
GAAAGTGCTTTGTAATGTTTTAACACACTCATTAATACTTTTATGGTTCGTAAAATTTGT
TATGATAGTTTTGTTTTCCGTTAATGATTAGAATGTGTGTTATTACATAAATTGATACCA
AACGGAGTATTTATTTAAATCATGAACATTTATTTAAAAGTTGAAATGATTTTCATTCAA
CATTTCCTTACAAAAATTAATATAAACTTACCTATATATTTTTAAAATATTTACTCTTAC
GATTTGCTTTACAAGAATGTATTTAAAAAGACAAGATGTTTAGTTAAAAATTCAATTTCT
ATACTATGTCAATGAAGATATAATAATTTAATAAATTTAAATTAATATATTTTCGTACTT
TAAGTTAAATTTGAAAATGATTGGCAATACTGTTACATTTAATGTTTTTGAAAGCTATTT
GCTAGTTGTTGCCAATCAGTCAATTTCGATTTGAAAAAAAGAAAATGTCATAAATATGAC
CTAAAAAAAGTTTTGATTAAAGAATAGAATGTTTGACAAAAGCTTCTTTAAAGAAAATGA
AAACTTACAATAATCTTAAAGTTATAAATAACTATAGCACATCACATTTCACTCAGAAGA
TATAATAAAATATTAAATTAAAATCAATCACAACAGTATAAATATATCAAAACAATCTTT
AAACAGATTCTTCTTTAGGTAGAATATTTCATTAAATAAAAAAATTCAAGAAAGTTTAGA
TATGCAATTTATAGAAGCTAAACTATCAATTGAAAATTTGATGGGTTTATGAATACATTC
ATAAAAAATGTATGCTCATTTGTTTCTTGCTATATGAAATCAATTTCAGTTTTTTCGATA
TCTAAATATAATTTTTTGAAAAAATGAAACACAAGAATATTTTTAGAAAAGATGTAATCT
TTTGGAAGA
>g11870.t4 Gene=g11870 Length=116
MSRWTPVIKDLMEDCIDEKLDQKHFPFLANRSGQTSYSVPTSARYGHWHKDKSQAPVIRN
VPRLIVFIVGGMSYSEMRCAYEVTNAYKNWEVIIGSSHILTPEGFLSDLGAISKDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11870.t4 | Coils | Coil | Coil | 114 | 116 | - |
| 5 | g11870.t4 | Gene3D | G3DSA:3.40.50.1910 | - | 1 | 116 | 3.8E-38 |
| 2 | g11870.t4 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 1 | 111 | 1.7E-38 |
| 3 | g11870.t4 | PANTHER | PTHR11679:SF27 | SYNTAXIN-BINDING PROTEIN 2 | 1 | 111 | 1.7E-38 |
| 1 | g11870.t4 | Pfam | PF00995 | Sec1 family | 2 | 108 | 5.1E-20 |
| 4 | g11870.t4 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 1 | 114 | 5.23E-33 |
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.
