Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicle-associated membrane protein/synaptobrevin-binding protein.

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 g12499 g12499.t10 isoform g12499.t10 24011380 24015729
chr_1 g12499 g12499.t10 exon g12499.t10.exon1 24011380 24011437
chr_1 g12499 g12499.t10 cds g12499.t10.CDS1 24011380 24011437
chr_1 g12499 g12499.t10 exon g12499.t10.exon2 24013414 24013566
chr_1 g12499 g12499.t10 cds g12499.t10.CDS2 24013414 24013566
chr_1 g12499 g12499.t10 exon g12499.t10.exon3 24013637 24014025
chr_1 g12499 g12499.t10 cds g12499.t10.CDS3 24013637 24014025
chr_1 g12499 g12499.t10 exon g12499.t10.exon4 24014081 24015729
chr_1 g12499 g12499.t10 cds g12499.t10.CDS4 24014081 24014275
chr_1 g12499 g12499.t10 TTS g12499.t10 24016365 24016365
chr_1 g12499 g12499.t10 TSS g12499.t10 NA NA

Sequences

>g12499.t10 Gene=g12499 Length=2249
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGGC
CCATTCACACAGCCTGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAAATC
GCATTCAAGATTAAAACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGAGTG
GTTGAACCAAAAAGCTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGATCCA
AATGAGAAGAATAAGCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAAATT
AATATTGAGCAATTATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTACGT
TGCACATTTGAGACACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTAACA
ACGCAAATGATTCAAAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTTGGA
ACATCTATTGTTGATTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACTGCT
GAAGTACGAGATCTTCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAACTAAAG
GAGCAAATTATTCGTTTGAAAGCTATGGTAGATAACCAAAAGGATACAACAAGTTCATCA
CCATCAGCTAAAATTATTTCAAATCCTTATTCACCACCACAACTTGGACAGCAGCAACAA
ATGCCCATTATATGGGTGATTGCAGCTGTTGCAATGGCCATTTTCGGTTTGATCCTTGGC
AAATTTGTCCTTTGAACGCATTAAGACTACAAAGCATGAAAAGCATACAGCAAACACAAG
CAACAAGAAAAATGAATGATAAAAAAAATATAAAAAAGTAGCTCATCGTTTTTATTTCCA
GCCAATGTGTCCAATTATGTGACAATTAATTATTCTTGTGGAGAGACATATGATGATGAT
GGTATAAAAATTAAAGTGTTGGGATGGGCGTAAAGAATCATAATTTACATTAAAGATTTT
TCCTAAAAACAAACATTATTACGACAGAAAGTTAAACTGTGGTCAAAACCAATAATGTAA
TGTCATATATTTCTTTTCAATTAGAAAATTGTATTTAATGAAAAATTTTGAAACTATAAA
ATATAACTCATCAATTGGATTGAATGATTCTTCTTTCAGAAGTGATTCATTCTCTCTCTC
TCTCCTTTCCTTTCCATAATCTTTTTATTTTATTAAAAGAAAAATAAAAATAATGAGTAA
AAAAGTCAAACTTAATATAAAGAAAACATATATATAAAAAAATAGAGAGCAGGTTCATTT
AATTAATTATTTAATCCATTAATGTTACACACAAATTCACTCATAAAAGAGAAGAAAAGA
AATTATCGCATTCATTTATGGATGATAATTTGAAAAGTAAACGAATTACTTTTAATTGTT
GCTTTATTGTTTCTTCTAATTTTGCAAGTTGCTATAATTCTTTTCCTTTCTCTAATATCA
TCATCTTATGTGTTTTTATACAAAAGAAAAATTTATATTTTTTTGTGTCAAATTTTTATG
TTATAATTTTTTTATATAATTTCTAAATGAATGAAAGAAATCCGTACGTCAAAAAACAAT
TTAAATGATAAAAAAAGTATAAAAACCAAGCATGTTAAAGTCAAAACTATTAAGAAATTC
ACCAAAGTGAGACTTATGTGTACACTATTAATGCAATAGCATTATTACACATTAAGTTCT
CACTATGAGTGAATAATATAAGAAAAAAATTTACATTATTTGATGGGGGGGTGGATGTTG
AACCATTTGCATTTTGTTACTCTTTTCATTTTATATTAAAACATATTGCAAAAAGATATG
AGAAAAAAATTCTACGGTAATTATGAATCAGACATCAAATTCTTTTGATTCTTTCCCTTC
AATAGATAATACATTTTGAATATATTTCATATTATGCAGAATGAATGAAAGAGAGATACC
TATAAAGAGAAATTTGCAAGAAAATTAATATGCTCTCTCGTGCACAACAAATTTAAACAA
GATTCAAAAGTGTGCATATTGATATAAAAAAATCTGCATATTATGAATTAAAAATTCAAA
ATTGAGTTTTGATTAATAAAATATAAAATAAAAGAAATGGGAAATGCTTAAAAATATAAA
AATATAAGTTTTTTTGTAACGTATTTTTCAGCGATTTGGATTTTAGTGTGCGTAGTTTCT
TTCTTTTCAATTTTTGATTTTTTCGAAGC

>g12499.t10 Gene=g12499 Length=264
MSKPENVLIIDPAQELKFRGPFTQPVTSHMSLKNPTDKKIAFKIKTTAPKKYCVRPNCGV
VEPKSSVEIAICLQPFVYDPNEKNKHKFMVQSMVVPEGEINIEQLWKDVSPEQLMDAKLR
CTFETPNEKVSEKSSVSQLTTQMIQNEATLSDSQLKTAVGTSIVDSSNKPSDVDFVRATA
EVRDLREENSKMHQENLELKEQIIRLKAMVDNQKDTTSSSPSAKIISNPYSPPQLGQQQQ
MPIIWVIAAVAMAIFGLILGKFVL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12499.t10 Coils Coil Coil 175 216 -
5 g12499.t10 Gene3D G3DSA:2.60.40.10 Immunoglobulins 1 125 3.1E-54
2 g12499.t10 PANTHER PTHR10809:SF131 VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A 1 145 3.4E-55
3 g12499.t10 PANTHER PTHR10809 VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN 1 145 3.4E-55
10 g12499.t10 PIRSF PIRSF019693 VAMP_assoc_prot 1 264 1.2E-63
1 g12499.t10 Pfam PF00635 MSP (Major sperm protein) domain 8 105 6.9E-34
8 g12499.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 242 -
9 g12499.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 263 -
7 g12499.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 264 264 -
12 g12499.t10 ProSiteProfiles PS50202 Major sperm protein (MSP) domain profile. 7 124 33.553
4 g12499.t10 SUPERFAMILY SSF49354 PapD-like 3 128 1.94E-43
11 g12499.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 241 263 -

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:0005789 endoplasmic reticulum membrane CC

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. There were no conditions that were differentially expressed