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.t3 isoform g12784.t3 26130980 26133966
chr_1 g12784 g12784.t3 exon g12784.t3.exon1 26130980 26131171
chr_1 g12784 g12784.t3 cds g12784.t3.CDS1 26130982 26131171
chr_1 g12784 g12784.t3 exon g12784.t3.exon2 26131366 26132128
chr_1 g12784 g12784.t3 cds g12784.t3.CDS2 26131366 26132128
chr_1 g12784 g12784.t3 exon g12784.t3.exon3 26132187 26132748
chr_1 g12784 g12784.t3 cds g12784.t3.CDS3 26132187 26132739
chr_1 g12784 g12784.t3 exon g12784.t3.exon4 26133762 26133966
chr_1 g12784 g12784.t3 TSS g12784.t3 26134105 26134105
chr_1 g12784 g12784.t3 TTS g12784.t3 NA NA

Sequences

>g12784.t3 Gene=g12784 Length=1722
ATGAGAAATTATTGGGCATTAGCATTGATTTCTTTATTAATAATTAAAATAGTATTAGTC
AATGCAAACAGCAAGTGTAAGAAAAGAAACTAAAATATTTATTGATAAAATTACCTAAAC
TATTCTATTTTTAGATTGCGTGAATCAGGATACATGTGATAAATGCTTAAATCAACATCC
AACATGTGCATGGTGTTCTGATCGTCTCTATGAAATGCGAAGGGCGAGATGCATGACAGA
GAAAGATTTGTTAGAGGCAAATTGTCGAAAAGAGTTCATTCAGATCAACCATTATGAGCC
TATGAGTAATGTCAGAGATGATGACTTGCGTGACTTCAATAAAGATTTTGATTCAGTGCA
GATACGACCACAAAGTGTTCGTATGAAATTGCAGAAAAATCGACAGCAGACGGTTAAATT
GAAATATAAGCCTGCAAAGAATTATCCACTTGATCTTTATCTTCTCATGGATTTAACTTG
GTCAATGCGTGACGATAAAGAAACTTTAGTAAAAATGGGTGGCAGTTTGAGCACATCACT
TAAGAATTTGACTGAAAACTTTCGTCTTGGCTTTGGGTCATTTGCTGATAAACCAATTGC
ACCTTATATTAATCCTGGCACTGAAGACAATCCATGTAAACTCGTACAAGAAACTTGTCT
ACCAACTTATGGCTTCAAGCATAAACTTGCAATGACAGACAACATTCAAGAGTTCATTAC
AAAGGTCAATGGAAGTGAAATTACTGGAAATTTGGATAATTTAGAAGGCGGTCTTGATGC
ACTCATGCAAGTGCTAGTATGTAGAGAAGAAATTGGTTGGAATGATAAAACAAGAAAAAT
TGTCGTATTTGCAACTGATGGACCAATGCATTTTGCTGGTGATGGTTTGCTTGCCGGATT
GGTAAAAAAGAATGATAAAAGCTGTCATTTGAGTGATAAAGGAGAATATATGGCTTCATT
GGAGTACGATTATCCTTCACTTGAAGAAATTTATCGTGAATTACTCCGAACGAAAGTTAG
TGTCATTTTTGCTGTCACATCTGATGTCATTTATCACTATGATCAAATGCATGAGATTAT
GGAAGAGATTACAAGTGTAGGCCAACTTGCAGCTGATTCTTCTAACATTTTACAGCTTGT
TGAGCAAGGTTTTAAACAAGCAGTTAAAAGAGCACAATTTCAAGATGATGCACCAGATTA
TTTGAGGGTTGAATATAAAACCAATTGTGGTGGAAAATATGAAACTTTACAAGACACAAA
CAAGTGTGATAATATTGAAATTGGTAAAGAATATGAATTTGATGTTGGAATTACTTTATT
AAAATATCCAGATGATGGTGCAAAGAGTGTCAAAATAAAAATTGAAGAAGCAAATATCGA
CGCTGAAGCAACAGAAATTGACATTGAAATTGATTATCCATGCACTAATTGTTTGGCACA
TCCTGGTGAAATTGCATCAGCATTGTGCAGTCGAAATGGCGAATACAAATGTGGAGCATG
CATTTGTGACAGTGGTTATGTTGGTAAACAGTGTGAATGCAATTTACAAGAATATTCAAG
CAGCAAGGAACTTGATAATCAATGTCGTGAGCCAAAAATAACTAATAATAACGAGACAAA
ACTTATGCCACCATGCTCGGATCGTGGTGAATGCCTCTGTGGAGAATGTTTCTGTAATGC
AAATTACGAGGGAAAATATTGTGAATGTGAAACCTGTCCAGT

>g12784.t3 Gene=g12784 Length=502
MRRARCMTEKDLLEANCRKEFIQINHYEPMSNVRDDDLRDFNKDFDSVQIRPQSVRMKLQ
KNRQQTVKLKYKPAKNYPLDLYLLMDLTWSMRDDKETLVKMGGSLSTSLKNLTENFRLGF
GSFADKPIAPYINPGTEDNPCKLVQETCLPTYGFKHKLAMTDNIQEFITKVNGSEITGNL
DNLEGGLDALMQVLVCREEIGWNDKTRKIVVFATDGPMHFAGDGLLAGLVKKNDKSCHLS
DKGEYMASLEYDYPSLEEIYRELLRTKVSVIFAVTSDVIYHYDQMHEIMEEITSVGQLAA
DSSNILQLVEQGFKQAVKRAQFQDDAPDYLRVEYKTNCGGKYETLQDTNKCDNIEIGKEY
EFDVGITLLKYPDDGAKSVKIKIEEANIDAEATEIDIEIDYPCTNCLAHPGEIASALCSR
NGEYKCGACICDSGYVGKQCECNLQEYSSSKELDNQCREPKITNNNETKLMPPCSDRGEC
LCGECFCNANYEGKYCECETCP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g12784.t3 CDD cd00198 vWFA 79 216 0.0004501
19 g12784.t3 Gene3D G3DSA:2.60.40.1510 ntegrin 47 434 0.0000000
21 g12784.t3 Gene3D G3DSA:3.40.50.410 - 74 320 0.0000000
20 g12784.t3 Gene3D G3DSA:2.10.25.10 Laminin 448 500 0.0000000
4 g12784.t3 PANTHER PTHR10082:SF59 INTEGRIN BETA-NU 1 501 0.0000000
5 g12784.t3 PANTHER PTHR10082 INTEGRIN BETA SUBUNIT 1 501 0.0000000
8 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 6 25 0.0000000
11 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 49 62 0.0000000
13 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 77 95 0.0000000
10 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 117 136 0.0000000
12 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 148 167 0.0000000
6 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 181 203 0.0000000
9 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 208 223 0.0000000
14 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 252 275 0.0000000
7 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 289 313 0.0000000
15 g12784.t3 PRINTS PR01186 Integrin beta subunit signature 474 487 0.0000000
2 g12784.t3 Pfam PF00362 Integrin beta chain VWA domain 74 317 0.0000000
3 g12784.t3 Pfam PF18372 Integrin beta epidermal growth factor like domain 1 411 435 0.0000014
1 g12784.t3 Pfam PF07974 EGF-like domain 473 496 0.0000070
17 g12784.t3 SMART SM00187 INB_2 2 406 0.0000000
18 g12784.t3 SMART SM00327 VWA_4 78 313 0.0016000
16 g12784.t3 SUPERFAMILY SSF53300 vWA-like 74 315 0.0000000

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