Gene loci information

Transcript annotation

  • This transcript has been annotated as Integrin beta-nu.

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 g12784 g12784.t4 isoform g12784.t4 26132113 26133966
chr_1 g12784 g12784.t4 exon g12784.t4.exon1 26132113 26132128
chr_1 g12784 g12784.t4 cds g12784.t4.CDS1 26132115 26132128
chr_1 g12784 g12784.t4 exon g12784.t4.exon2 26132187 26132748
chr_1 g12784 g12784.t4 cds g12784.t4.CDS2 26132187 26132748
chr_1 g12784 g12784.t4 exon g12784.t4.exon3 26133762 26133832
chr_1 g12784 g12784.t4 cds g12784.t4.CDS3 26133762 26133832
chr_1 g12784 g12784.t4 exon g12784.t4.exon4 26133891 26133966
chr_1 g12784 g12784.t4 cds g12784.t4.CDS4 26133891 26133966
chr_1 g12784 g12784.t4 TSS g12784.t4 26134105 26134105
chr_1 g12784 g12784.t4 TTS g12784.t4 NA NA

Sequences

>g12784.t4 Gene=g12784 Length=725
ATGAGAAATTATTGGGCATTAGCATTGATTTCTTTATTAATAATTAAAATAGTATTAGTC
AATGCAAACAGCAAGTATTGCGTGAATCAGGATACATGTGATAAATGCTTAAATCAACAT
CCAACATGTGCATGGTGTTCTGATCGTCTCTATGAAATGCGAAGGGCGAGATGCATGACA
GAGAAAGATTTGTTAGAGGCAAATTGTCGAAAAGAGTTCATTCAGATCAACCATTATGAG
CCTATGAGTAATGTCAGAGATGATGACTTGCGTGACTTCAATAAAGATTTTGATTCAGTG
CAGATACGACCACAAAGTGTTCGTATGAAATTGCAGAAAAATCGACAGCAGACGGTTAAA
TTGAAATATAAGCCTGCAAAGAATTATCCACTTGATCTTTATCTTCTCATGGATTTAACT
TGGTCAATGCGTGACGATAAAGAAACTTTAGTAAAAATGGGTGGCAGTTTGAGCACATCA
CTTAAGAATTTGACTGAAAACTTTCGTCTTGGCTTTGGGTCATTTGCTGATAAACCAATT
GCACCTTATATTAATCCTGGCACTGAAGACAATCCATGTAAACTCGTACAAGAAACTTGT
CTACCAACTTATGGCTTCAAGCATAAACTTGCAATGACAGACAACATTCAAGAGTTCATT
ACAAAGGTCAATGGAAGTGAAATTACTGGAAATTTGGATAATTTAGAAGGCGGTCTTGAT
GCACT

>g12784.t4 Gene=g12784 Length=241
MRNYWALALISLLIIKIVLVNANSKYCVNQDTCDKCLNQHPTCAWCSDRLYEMRRARCMT
EKDLLEANCRKEFIQINHYEPMSNVRDDDLRDFNKDFDSVQIRPQSVRMKLQKNRQQTVK
LKYKPAKNYPLDLYLLMDLTWSMRDDKETLVKMGGSLSTSLKNLTENFRLGFGSFADKPI
APYINPGTEDNPCKLVQETCLPTYGFKHKLAMTDNIQEFITKVNGSEITGNLDNLEGGLD
A

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12784.t4 Gene3D G3DSA:3.30.1680.10 - 23 77 1.3E-11
16 g12784.t4 Gene3D G3DSA:3.40.50.410 - 126 241 9.6E-40
3 g12784.t4 PANTHER PTHR10082:SF59 INTEGRIN BETA-NU 12 241 1.5E-84
4 g12784.t4 PANTHER PTHR10082 INTEGRIN BETA SUBUNIT 12 241 1.5E-84
11 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 30 46 4.9E-37
10 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 58 77 4.9E-37
7 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 101 114 4.9E-37
6 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 129 147 4.9E-37
9 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 169 188 4.9E-37
8 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 200 219 4.9E-37
5 g12784.t4 PRINTS PR01186 Integrin beta subunit signature 233 241 4.9E-37
1 g12784.t4 Pfam PF17205 Integrin plexin domain 27 69 1.5E-11
2 g12784.t4 Pfam PF00362 Integrin beta chain VWA domain 126 241 4.8E-43
19 g12784.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
20 g12784.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
21 g12784.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 15 -
22 g12784.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 22 -
18 g12784.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 241 -
23 g12784.t4 SMART SM00187 INB_2 32 241 3.0E-14
12 g12784.t4 SUPERFAMILY SSF103575 Plexin repeat 23 74 4.19E-12
13 g12784.t4 SUPERFAMILY SSF53300 vWA-like 126 241 8.7E-30
15 g12784.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
14 g12784.t4 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 22 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed