Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t7 TSS g3701.t7 27553677 27553677
chr_3 g3701 g3701.t7 isoform g3701.t7 27554270 27555379
chr_3 g3701 g3701.t7 exon g3701.t7.exon1 27554270 27554361
chr_3 g3701 g3701.t7 cds g3701.t7.CDS1 27554275 27554361
chr_3 g3701 g3701.t7 exon g3701.t7.exon2 27554569 27554608
chr_3 g3701 g3701.t7 cds g3701.t7.CDS2 27554569 27554608
chr_3 g3701 g3701.t7 exon g3701.t7.exon3 27554694 27554813
chr_3 g3701 g3701.t7 cds g3701.t7.CDS3 27554694 27554813
chr_3 g3701 g3701.t7 exon g3701.t7.exon4 27554871 27555379
chr_3 g3701 g3701.t7 cds g3701.t7.CDS4 27554871 27555379
chr_3 g3701 g3701.t7 TTS g3701.t7 27555715 27555715

Sequences

>g3701.t7 Gene=g3701 Length=761
AAAGTATGAGTGGTAGTATATGGAATCAAATTCCTTGTTGGAATCGCAACTGGGAGGTTG
TTGTAGATTTTAAAGTAGCAGGAAAAGGAAAAGATTTATTCGGCGATGGTTTTGTTGTTT
GGTATGCTAGAGATCGTATGATCACCGGTCCAGTATTTGGTAGTAAAGATTTTTTCAGTG
GCCTAGCAATTATTGTAGATACATATAGTAATCATAATGGACCACATAATCACCAACATC
CTTATATTTCTGCTATGGTGAACAATGGAACACTTACATATGATCATGATCGAGATGGAA
CACATACACAATTAGCAGGATGTGAAGCTCGGTTTAGAAATGTTGAACATACGACACAAT
TGAAAATTAGATACGAAAACGATGTGCTCTCTGTACATACAGATCTTGAGAACAAAAATG
AATGGAAAGAATGTTTTACCGTTGATGGTGTTGAACTTCCAACTGGTTATTATTTTGGTG
CATCAGCTACAACAGGCGATCTCAGTGATAATCATTTAATTAACTCCATAAAATTCTTCG
AGCTTGAAGGTGCAACTACTGCTGAACGCTCTCAAATTATTCCGCATGCTGCAAAATTTG
AAGAGCCTCGCGAGCACGTAGACGACCCAAAGCCGGGTTGGTCGAATCTTAAAATTTTTA
TAGTCATTCTTTTTGGAATGATCGGCGCTGTAATTCTCAGCATTGGAGGATATATGTACT
ATGAAAAATATCAACAGAATAAAAAGAAAAGATTTTACTGA

>g3701.t7 Gene=g3701 Length=251
MSGSIWNQIPCWNRNWEVVVDFKVAGKGKDLFGDGFVVWYARDRMITGPVFGSKDFFSGL
AIIVDTYSNHNGPHNHQHPYISAMVNNGTLTYDHDRDGTHTQLAGCEARFRNVEHTTQLK
IRYENDVLSVHTDLENKNEWKECFTVDGVELPTGYYFGASATTGDLSDNHLINSIKFFEL
EGATTAERSQIIPHAAKFEEPREHVDDPKPGWSNLKIFIVILFGMIGAVILSIGGYMYYE
KYQQNKKKRFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3701.t7 Gene3D G3DSA:2.60.120.200 - 1 200 1.4E-77
2 g3701.t7 PANTHER PTHR12223 VESICULAR MANNOSE-BINDING LECTIN 2 251 2.7E-82
3 g3701.t7 PANTHER PTHR12223:SF36 VESICULAR INTEGRAL-MEMBRANE PROTEIN VIP36 2 251 2.7E-82
1 g3701.t7 Pfam PF03388 Legume-like lectin family 2 181 1.0E-77
9 g3701.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 216 -
10 g3701.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 217 239 -
8 g3701.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 240 251 -
7 g3701.t7 ProSiteProfiles PS51328 L-type lectin-like (leguminous) domain profile. 1 180 47.543
5 g3701.t7 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 2 180 1.4E-54
4 g3701.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 217 239 -

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