Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein ROP.

Parent gene

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.t1 TSS g11870.t1 18860436 18860436
chr_1 g11870 g11870.t1 isoform g11870.t1 18860526 18864790
chr_1 g11870 g11870.t1 exon g11870.t1.exon1 18860526 18860553
chr_1 g11870 g11870.t1 cds g11870.t1.CDS1 18860526 18860553
chr_1 g11870 g11870.t1 exon g11870.t1.exon2 18860955 18861119
chr_1 g11870 g11870.t1 cds g11870.t1.CDS2 18860955 18861119
chr_1 g11870 g11870.t1 exon g11870.t1.exon3 18861194 18861263
chr_1 g11870 g11870.t1 cds g11870.t1.CDS3 18861194 18861263
chr_1 g11870 g11870.t1 exon g11870.t1.exon4 18861327 18861412
chr_1 g11870 g11870.t1 cds g11870.t1.CDS4 18861327 18861412
chr_1 g11870 g11870.t1 exon g11870.t1.exon5 18861570 18861673
chr_1 g11870 g11870.t1 cds g11870.t1.CDS5 18861570 18861673
chr_1 g11870 g11870.t1 exon g11870.t1.exon6 18863329 18863964
chr_1 g11870 g11870.t1 cds g11870.t1.CDS6 18863329 18863964
chr_1 g11870 g11870.t1 exon g11870.t1.exon7 18864030 18864311
chr_1 g11870 g11870.t1 cds g11870.t1.CDS7 18864030 18864311
chr_1 g11870 g11870.t1 exon g11870.t1.exon8 18864377 18864790
chr_1 g11870 g11870.t1 cds g11870.t1.CDS8 18864377 18864790
chr_1 g11870 g11870.t1 TTS g11870.t1 18865384 18865384

Sequences

>g11870.t1 Gene=g11870 Length=1785
ATGGCTTTAAAAGTGCTCGTTGGTCAAAAAATTATGAATGAAGTCATCAAATATAAAGGA
CCTGCAAAAAAATCGCAGCCTGGTCAAAAATCATCAAATGTGGAATGGCGTGTCTTGGTT
GTTGATAAACTTTCAATGCGAATGGTCTCAGCCTGTACTAAAATGCACGACCTTTCAGCT
GAGGCAATAACATTGGTTGAAGATATTAACAAGAAACGCGAACCGTTACAAACAATGGAA
GCAGTATATTTGATAACACCCTGTGAAGAGTCAGTGCGGGGATTAATTCGAGATTTTGAG
TCACCCACTCGTCCACTTTATAAAGCAGCTCATGTTTTCTTCACAGAAGCAATTCCTGAT
AGTTTATTTGAAAAAATTAAGGGACAATCAGTTGTAAAATATATGAGAGCGTGTAAAGAA
ATTAACATATCATTTATACCATATGAAAAACAGGTCTTCTCATTGGATTCACCGGACACA
TTTCAATGTAGCTATTCGCCAAGCTTGAGGTCCGCTCGAGTTGGCAACATGGAGCGTATC
GCCGAACAGGTCGCTACGCTTTGTTCCACTTTGGGCGAGTATCCTTCTATACGTTATCGC
AGTGATTGGGAGCGTAATGTTGAATTGGCCCAATTGATACAACAAAAATTGGACGCCTAC
AAAGCCGATGAACCAACAATGGGTGAAGGACCAGAAAAGGCCAAATCAACATTGTTGATT
CTGGATCGTGGCTTTGATTGCGTTTCTCCATTACTGCATGAATTAACGTTACAAGCAATG
GCATATGATTTGCTACCAATTTCAAATGATGTCTACAAGTATGAAAATCAAGGCGCAGAG
AAGGAAGTCTTATTGGATGAGAATGATGAATTGTGGTGTGAATTGCGTCATCAACATATT
GCAGTTGTTTCTCAAAAGGTTACCGCTAATTTGAAGAATTTTACCGAATCTAAGCGCATG
TCTTCAACTGATAAAGCATCAATGAGAGATCTCTCGCAAATGATTAAAAAAATGCCGCAG
TATCAAAAAGAACTCTCAAAATATGCAACACATTTGCATTTGGCCGAAGATTGTATGAAA
GCTTATCAAGGTTACATTGATAAATTATGTCGGGTTGAACAAGATTTGGCTATGGGAACA
GATGCTGAAGGAGAAAAGATCAAAGATCATATGCGTAATATTGTTCCAATTCTCTTAGAT
ACATCTGTTTCTAATTACGATAAAGTACGCATCATTGCACTTTATGTGATGATTAAAAAT
GGCATTTCTGAAGAAAATTTTACAAAATTAGCAACACATGCAGGAATTGAACAACGTGAA
CGTGAAATGATTTTAAATTTAAGCCATTTGGGTATTAATGTAATTTCAGATGGAAGTCGT
CGAAAGCAATATCAAATTCCTCGTAAAGAAAGAATCACAGAGCAAACGTATCAAATGTCT
CGCTGGACACCAGTTATAAAAGATCTCATGGAAGATTGTATTGATGAGAAATTGGATCAA
AAACATTTTCCATTCTTGGCAAATCGCTCGGGTCAAACATCTTATAGTGTTCCAACAAGC
GCTCGTTATGGTCATTGGCACAAAGATAAATCACAGGCTCCTGTTATCCGAAATGTACCA
CGTCTTATTGTCTTCATAGTTGGTGGAATGAGTTATTCAGAAATGCGATGTGCATATGAA
GTTACAAACGCTTATAAAAATTGGGAAGTAATAATTGGATCTTCACACATTTTAACTCCT
GAAGGCTTTTTAAGTGATTTGGGTGCAATTTCAAAGGATGATTAA

>g11870.t1 Gene=g11870 Length=594
MALKVLVGQKIMNEVIKYKGPAKKSQPGQKSSNVEWRVLVVDKLSMRMVSACTKMHDLSA
EAITLVEDINKKREPLQTMEAVYLITPCEESVRGLIRDFESPTRPLYKAAHVFFTEAIPD
SLFEKIKGQSVVKYMRACKEINISFIPYEKQVFSLDSPDTFQCSYSPSLRSARVGNMERI
AEQVATLCSTLGEYPSIRYRSDWERNVELAQLIQQKLDAYKADEPTMGEGPEKAKSTLLI
LDRGFDCVSPLLHELTLQAMAYDLLPISNDVYKYENQGAEKEVLLDENDELWCELRHQHI
AVVSQKVTANLKNFTESKRMSSTDKASMRDLSQMIKKMPQYQKELSKYATHLHLAEDCMK
AYQGYIDKLCRVEQDLAMGTDAEGEKIKDHMRNIVPILLDTSVSNYDKVRIIALYVMIKN
GISEENFTKLATHAGIEQREREMILNLSHLGINVISDGSRRKQYQIPRKERITEQTYQMS
RWTPVIKDLMEDCIDEKLDQKHFPFLANRSGQTSYSVPTSARYGHWHKDKSQAPVIRNVP
RLIVFIVGGMSYSEMRCAYEVTNAYKNWEVIIGSSHILTPEGFLSDLGAISKDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11870.t1 Gene3D G3DSA:3.40.50.2060 - 1 140 0
6 g11870.t1 Gene3D G3DSA:3.40.50.1910 - 143 587 0
8 g11870.t1 Gene3D G3DSA:3.90.830.10 Syntaxin Binding Protein 1; Chain A 254 363 0
5 g11870.t1 Gene3D G3DSA:1.25.40.60 - 364 483 0
2 g11870.t1 PANTHER PTHR11679:SF35 SYNTAXIN-BINDING PROTEIN 1 8 588 0
3 g11870.t1 PANTHER PTHR11679 VESICLE PROTEIN SORTING-ASSOCIATED 8 588 0
9 g11870.t1 PIRSF PIRSF005715 VPS45_Sec1 1 594 0
1 g11870.t1 Pfam PF00995 Sec1 family 37 586 0
4 g11870.t1 SUPERFAMILY SSF56815 Sec1/munc18-like (SM) proteins 10 592 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

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.

Raw TPM values