General information for g3701.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vesicular integral-membrane protein VIP36.
Parent gene
- The parent gene g3701 is located on chr_3: 27554875..27556092 (+ 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_3 | g3701 | g3701.t1 | TSS | g3701.t1 | 27553677 | 27553677 |
| chr_3 | g3701 | g3701.t1 | isoform | g3701.t1 | 27553745 | 27555379 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon1 | 27553745 | 27553848 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS1 | 27553745 | 27553848 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon2 | 27553929 | 27553960 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS2 | 27553929 | 27553960 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon3 | 27554097 | 27554174 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS3 | 27554097 | 27554174 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon4 | 27554264 | 27554361 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS4 | 27554264 | 27554361 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon5 | 27554569 | 27554608 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS5 | 27554569 | 27554608 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon6 | 27554694 | 27554813 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS6 | 27554694 | 27554813 |
| chr_3 | g3701 | g3701.t1 | exon | g3701.t1.exon7 | 27554871 | 27555379 |
| chr_3 | g3701 | g3701.t1 | cds | g3701.t1.CDS7 | 27554871 | 27555379 |
| chr_3 | g3701 | g3701.t1 | TTS | g3701.t1 | 27555715 | 27555715 |
Sequences
>g3701.t1 Gene=g3701 Length=981
ATGGAGAAACTTAATAAAATAAGTCAATATCTAGCATGTGTTCTTATTATCCATATTGTG
ACATGTTTAGCTCAAAATCCTGTAAGAGAACACATTTATAATAGAAGAGAACATTCACTT
ATAAAACCATTTTTGACTGCTGGACTTTCTGTACCTTATTGGGATTACACTGGTTCTGTT
ATTTTTACACAAAATTATGTTCGTCTAACTCCAGATGAACAAAGTATGAGTGGTAGTATA
TGGAATCAAATTCCTTGTTGGAATCGCAACTGGGAGGTTGTTGTAGATTTTAAAGTAGCA
GGAAAAGGAAAAGATTTATTCGGCGATGGTTTTGTTGTTTGGTATGCTAGAGATCGTATG
ATCACCGGTCCAGTATTTGGTAGTAAAGATTTTTTCAGTGGCCTAGCAATTATTGTAGAT
ACATATAGTAATCATAATGGACCACATAATCACCAACATCCTTATATTTCTGCTATGGTG
AACAATGGAACACTTACATATGATCATGATCGAGATGGAACACATACACAATTAGCAGGA
TGTGAAGCTCGGTTTAGAAATGTTGAACATACGACACAATTGAAAATTAGATACGAAAAC
GATGTGCTCTCTGTACATACAGATCTTGAGAACAAAAATGAATGGAAAGAATGTTTTACC
GTTGATGGTGTTGAACTTCCAACTGGTTATTATTTTGGTGCATCAGCTACAACAGGCGAT
CTCAGTGATAATCATTTAATTAACTCCATAAAATTCTTCGAGCTTGAAGGTGCAACTACT
GCTGAACGCTCTCAAATTATTCCGCATGCTGCAAAATTTGAAGAGCCTCGCGAGCACGTA
GACGACCCAAAGCCGGGTTGGTCGAATCTTAAAATTTTTATAGTCATTCTTTTTGGAATG
ATCGGCGCTGTAATTCTCAGCATTGGAGGATATATGTACTATGAAAAATATCAACAGAAT
AAAAAGAAAAGATTTTACTGA
>g3701.t1 Gene=g3701 Length=326
MEKLNKISQYLACVLIIHIVTCLAQNPVREHIYNRREHSLIKPFLTAGLSVPYWDYTGSV
IFTQNYVRLTPDEQSMSGSIWNQIPCWNRNWEVVVDFKVAGKGKDLFGDGFVVWYARDRM
ITGPVFGSKDFFSGLAIIVDTYSNHNGPHNHQHPYISAMVNNGTLTYDHDRDGTHTQLAG
CEARFRNVEHTTQLKIRYENDVLSVHTDLENKNEWKECFTVDGVELPTGYYFGASATTGD
LSDNHLINSIKFFELEGATTAERSQIIPHAAKFEEPREHVDDPKPGWSNLKIFIVILFGM
IGAVILSIGGYMYYEKYQQNKKKRFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3701.t1 | Gene3D | G3DSA:2.60.120.200 | - | 51 | 275 | 6.3E-90 |
| 2 | g3701.t1 | PANTHER | PTHR12223 | VESICULAR MANNOSE-BINDING LECTIN | 10 | 325 | 5.6E-102 |
| 3 | g3701.t1 | PANTHER | PTHR12223:SF28 | RE50040P | 10 | 325 | 5.6E-102 |
| 1 | g3701.t1 | Pfam | PF03388 | Legume-like lectin family | 35 | 256 | 1.2E-93 |
| 9 | g3701.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 10 | g3701.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 10 | - |
| 11 | g3701.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 11 | 19 | - |
| 13 | g3701.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 20 | 24 | - |
| 8 | g3701.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 291 | - |
| 12 | g3701.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 314 | - |
| 7 | g3701.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 315 | 326 | - |
| 15 | g3701.t1 | ProSiteProfiles | PS51328 | L-type lectin-like (leguminous) domain profile. | 32 | 255 | 54.026 |
| 4 | g3701.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 31 | 255 | 4.45E-67 |
| 5 | g3701.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 14 | g3701.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 314 | - |
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 transcript has been annotated with K10082 (lectin, mannose-binding 2)
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.
