HsaINT0082792 @ hg19
Intron Retention
Gene
ENSG00000150093 | ITGB1
Description
integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [Source:HGNC Symbol;Acc:6153]
Coordinates
chr10:33197296-33199383:-
Coord C1 exon
chr10:33199151-33199383
Coord A exon
chr10:33197463-33199150
Coord C2 exon
chr10:33197296-33197462
Length
1688 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAA
5' ss Score
6.68
3' ss Seq
ATTACCTTCTTATTTTCCAGAGT
3' ss Score
10.2
Exon sequences
Seq C1 exon
AGAATGTGTTCAGTGCAGAGCCTTCAATAAAGGAGAAAAGAAAGACACATGCACACAGGAATGTTCCTATTTTAACATTACCAAGGTAGAAAGTCGGGACAAATTACCCCAGCCGGTCCAACCTGATCCTGTGTCCCATTGTAAGGAGAAGGATGTTGACGACTGTTGGTTCTATTTTACGTATTCAGTGAATGGGAACAACGAGGTCATGGTTCATGTTGTGGAGAATCCAG
Seq A exon
GTAGAAATGCGATGATTGCAGACATTCTTTTCATATCTTGTATGTCTTGTTTCTGCTTATTTAGGCCTAACATCCAGAAACAGCCTCCAGCTGGAATATTTTAGGTCAAGTTGGGAAATTTTTCATCTCTCAAAGCTTAAAATATTATCTAATTAACTGTATAAGAAATAAGGAAAAGAGAGTTCCACTTTTAAGTTTTCTGAGTGGAGAGTTTGAAGATTAAATACAGTGATTTATATAAGACGCTTAGTGATTTATATAAGACACTTAGAACGATGCCTGACACCAAGTGCATATTAAGAGTTTTTTGATGATTGATGATTTTAAAATTAGAGCTTGATTTAAGCTTGAATACTGGGAAAGATAATTTGTTAAAGGATATTAATATAAAGTGTTGAATTTGTTCAACTTCTCCGGAGGTGAAACTTTTTTTTTTTAATCTTAGTTTTCCTAGTAGCCTTTTTGTAGATTCTTTGGAATTTTCTACCATAGTGTACATGTTTTTGTGTGAACATAAGCTTTCATTTCTCTTGGGTAAATACTAAAAATGGCATTTTGGAGCATATGGTAAGCATATGTTTAACTTTGTTAAGAAGCTGCCAGACTCTTAGACTCCCATACTGTTTTGAATTATCAGCTAGGTGTTTTGCAAATATTGTCTCCCAGCCTGTGTCTCCTTATCATTTCATTTTTTTAAGTGTCTTCTGAACACCACAGGTTTTAATTTTGATTAAGTACAGTTTACCAAGTTTTTCTTCTGTGGCTCTTGCTTTTACATTGTCTTTAAGAACTCTGCCTAACCCAAGATTATAAGGATTTTTCTCCTCTGTTTTTTGGTAGAAGTTTTATAGTTTCTGGGGTTTCACATTTAGATCTGTAACTCATTTTGAGTTAGTGTGTGACAAAAGGCTCAGTTTTTTTCATGTCAGTGTCCACTTGTTCTAGGGGCATTTGTTGAAAAAAGACTGTCTTTTCTCCACCTTTGTTGAACATCAGGTGACCTTACATGTGTAGGCCTGTTTCTGACTCTGTATTCTGTTCCATGTATCTGAGTGTTAGCTATACCACATGGTCTTGTAGCTTTCTTTATAGCTAGGCCTGAAAGCAGGGTCTTCCAACTTTATTCTTTTACAAAAGTGTTTTTGAGACACTTCCTTAGTTCCCTGCCTTCCATGTAAATTTTAGAAGTGGCTTACTGATTGCTACAGAAGTTCTGCCAGGAGTTTGAGTGGGATACCATTGAGTTTATAGATCAAATTGGGAAGAATTGACGTCTTAACGGTATTAGGTTTTGTAACTCCTGCACATGGAATATCTCTCCATTTATTCAGTCTGAAAGATTTCTTTTTATCAGTATTTAGTAATTCTTAACATGCAAATCTTGCATATATTTTGTTAGACTTATATGTAAGTTTTTCATGCTTTTTCATTCTGTAGTAAATATTACTGTTTAAAAACTTATATTTTCAATATGTAGAAATAAATTATATATATAGAAAAATACATGATTTTTGTTCATTGATCATGTATCCTGCAACCTTGTAAACTCACTTGTTAGTTCTAAGAGCTATTTTATAGATTCTTTGGGATAGTGTGCGTTCACTCTCTTGGGTGTTTATTCCTGTATGTTTTTTATAAGACACTGCACAGCTCTTTGTGGTGCTCATTATTACCTTCTTATTTTCCAG
Seq C2 exon
AGTGTCCCACTGGTCCAGACATCATTCCAATTGTAGCTGGTGTGGTTGCTGGAATTGTTCTTATTGGCCTTGCATTACTGCTGATATGGAAGCTTTTAATGATAATTCATGACAGAAGGGAGTTTGCTAAATTTGAAAAGGAGAAAATGAATGCCAAATGGGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-ITGB1:NM_002211:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=FE(87.6=100)
A:
NA
C2:
PF079657=Integrin_B_tail=PD(6.7=10.7),PF087256=Integrin_b_cyt=PU(53.2=44.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCAGTGCAGAGCCTTCA
R:
AGCAAACTCCCTTCTGTCATGA
Band lengths:
356-2044
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)