HsaINT0082791 @ 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
chr10:33199151-33200598:-
Coord C1 exon
chr10:33200376-33200598
Coord A exon
chr10:33199384-33200375
Coord C2 exon
chr10:33199151-33199383
Length
992 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
ATTTGTGTTTTTTGTAACAGAGA
3' ss Score
8.6
Exon sequences
Seq C1 exon
GAAATGGTGTTTGCAAGTGTCGTGTGTGTGAGTGCAACCCCAACTACACTGGCAGTGCATGTGACTGTTCTTTGGATACTAGTACTTGTGAAGCCAGCAACGGACAGATCTGCAATGGCCGGGGCATCTGCGAGTGTGGTGTCTGTAAGTGTACAGATCCGAAGTTTCAAGGGCAAACGTGTGAGATGTGTCAGACCTGCCTTGGTGTCTGTGCTGAGCATAA
Seq A exon
GTAAGTATTTCCTAATTGCTTGAAATAGTTGATACTTCCTCTTGGCTCTCCTAAGCCTGTATTGTTTCTAGAACCAGAACAGTGCCAATATTAAAATATACTGTAAATAAAATGCCTGCCATGTGGAAGCCTACTCTTTAATTCTTAAAAGTTCTTTCTCAACAGCTAGTATATATTACATGGTATGAAGTGTGTCATGTGAGAGTTGTACTATTATTTTGATCTGAATGTGCTAGATAATTGAATTTACATGGTAACCTTTATTTTGGCAATTAAGATTTAATTTAATTTAATTTGTCATTACCAATTTCTTAATTACTGTCTTTTGACAAAACTAAGCCAAATTAAAGATTTTTCCTCTTGAAGGATTATTATACTAGTAACATATTATTTAAATTATTATGATTTTGGCCGAGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCGAGACAGGTGGATCACTTAAGGTCAGGAGTTTGAGACCAGTCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGATATGGTGGTGTGTGCCTGTAATCTCAACTACTTGGGAGGTTGAGGCTTGCTTGAACCCGAGAGGCAGAGGTTACAGTGAGCCAAGGTCACACCACTGCACTGCCTGGATGACAGAACAAGACTCCATCGCAAAAAAAAAATTATTATGATTTTATGTTACATATTTAATATGTGATAGGGCTAATTTATTTTACTATCTTTTATTTCTTAATAGGGTTTTAATTTGAACTGTAATAAATCTTTAATTTTATTATGGAAATTAGCATCTTTTTACATAATTTTTCTATCCACAAATGTAATGTTCCTCTTCATTTATTGAAATCTTCCTTCATAGCTGTTTGTTCAATTTGGTCACAAGAGTTTAGCATGGGAAATATGTTTAAGCAAATATTTACTGAAATAATAAAATGTAAATATCATAATTTGTGTTTTTTGTAACAG
Seq C2 exon
AGAATGTGTTCAGTGCAGAGCCTTCAATAAAGGAGAAAAGAAAGACACATGCACACAGGAATGTTCCTATTTTAACATTACCAAGGTAGAAAGTCGGGACAAATTACCCCAGCCGGTCCAACCTGATCCTGTGTCCCATTGTAAGGAGAAGGATGTTGACGACTGTTGGTTCTATTTTACGTATTCAGTGAATGGGAACAACGAGGTCATGGTTCATGTTGTGGAGAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-ITGB1:NM_002211:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.025
Domain overlap (PFAM):
C1:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
A:
NA
C2:
PF079657=Integrin_B_tail=FE(87.6=100)
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:
TTGCAAGTGTCGTGTGTGTGA
R:
GGGACACAGGATCAGGTTGGA
Band lengths:
350-1342
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)