Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative VIP36-like 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_3 g3701 g3701.t11 TSS g3701.t11 27553677 27553677
chr_3 g3701 g3701.t11 isoform g3701.t11 27554569 27555379
chr_3 g3701 g3701.t11 exon g3701.t11.exon1 27554569 27554608
chr_3 g3701 g3701.t11 exon g3701.t11.exon2 27554694 27554813
chr_3 g3701 g3701.t11 cds g3701.t11.CDS1 27554699 27554813
chr_3 g3701 g3701.t11 exon g3701.t11.exon3 27554871 27555379
chr_3 g3701 g3701.t11 cds g3701.t11.CDS2 27554871 27555379
chr_3 g3701 g3701.t11 TTS g3701.t11 27555715 27555715

Sequences

>g3701.t11 Gene=g3701 Length=669
GATTTATTCGGCGATGGTTTTGTTGTTTGGTATGCTAGAGATCGTATGATCACCGGTCCA
GTATTTGGTAGTAAAGATTTTTTCAGTGGCCTAGCAATTATTGTAGATACATATAGTAAT
CATAATGGACCACATAATCACCAACATCCTTATATTTCTGCTATGGTGAACAATGGAACA
CTTACATATGATCATGATCGAGATGGAACACATACACAATTAGCAGGATGTGAAGCTCGG
TTTAGAAATGTTGAACATACGACACAATTGAAAATTAGATACGAAAACGATGTGCTCTCT
GTACATACAGATCTTGAGAACAAAAATGAATGGAAAGAATGTTTTACCGTTGATGGTGTT
GAACTTCCAACTGGTTATTATTTTGGTGCATCAGCTACAACAGGCGATCTCAGTGATAAT
CATTTAATTAACTCCATAAAATTCTTCGAGCTTGAAGGTGCAACTACTGCTGAACGCTCT
CAAATTATTCCGCATGCTGCAAAATTTGAAGAGCCTCGCGAGCACGTAGACGACCCAAAG
CCGGGTTGGTCGAATCTTAAAATTTTTATAGTCATTCTTTTTGGAATGATCGGCGCTGTA
ATTCTCAGCATTGGAGGATATATGTACTATGAAAAATATCAACAGAATAAAAAGAAAAGA
TTTTACTGA

>g3701.t11 Gene=g3701 Length=207
MITGPVFGSKDFFSGLAIIVDTYSNHNGPHNHQHPYISAMVNNGTLTYDHDRDGTHTQLA
GCEARFRNVEHTTQLKIRYENDVLSVHTDLENKNEWKECFTVDGVELPTGYYFGASATTG
DLSDNHLINSIKFFELEGATTAERSQIIPHAAKFEEPREHVDDPKPGWSNLKIFIVILFG
MIGAVILSIGGYMYYEKYQQNKKKRFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3701.t11 Gene3D G3DSA:2.60.120.200 - 1 156 5.0E-58
2 g3701.t11 PANTHER PTHR12223 VESICULAR MANNOSE-BINDING LECTIN 2 207 4.5E-61
3 g3701.t11 PANTHER PTHR12223:SF36 VESICULAR INTEGRAL-MEMBRANE PROTEIN VIP36 2 207 4.5E-61
1 g3701.t11 Pfam PF03388 Legume-like lectin family 2 137 6.8E-59
9 g3701.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 172 -
10 g3701.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
8 g3701.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 196 207 -
7 g3701.t11 ProSiteProfiles PS51328 L-type lectin-like (leguminous) domain profile. 1 136 33.445
5 g3701.t11 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 3 136 1.71E-40
4 g3701.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -

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:0016020 membrane CC

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.

Raw TPM values