RnoINT0076459 @ rn6
Intron Retention
Gene
ENSRNOG00000004516 | Itgbl1
Description
integrin subunit beta like 1 [Source:RGD Symbol;Acc:1560635]
Coordinates
chr15:110376953-110378969:+
Coord C1 exon
chr15:110376953-110377066
Coord A exon
chr15:110377067-110378166
Coord C2 exon
chr15:110378167-110378969
Length
1100 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
CTGTGTTTACTTTATTGCAGGGA
3' ss Score
9.33
Exon sequences
Seq C1 exon
GTTCTTGTCATTGTGGAAAGTGCATTTGTTCTGGAGAAGAGTGGTATATTTCAGGGGAGTTTTGTGACTGTGATGACAGAGACTGTGACAAACACGACGGTCTCATTTGCACAG
Seq A exon
GTGCAGTATTGAACTACACTAATTGTTTTGGGCCACAAATGACAATTGAGTGAAATGACACCCACAACACACAGCTTTAGATAGGGCAGAGAGGGCAGCTCCCACACACTCAAATGAACAATGCCCATGTGTAGTAATTCTGAAAGGAAAAGTGAACATCTGTGAATACACACCAACATTTTCCCTAGAAGAATGCAAAGATATGAAGCCAGATTACATGAGTGTTGGAATATTTCTACAAGATAACCTGTTCTATAAACTCACACAAAGACAGTTATATGAAAAAAGAATTCTCTTGACAACCATTTCATCTTAATATGGTCCAGATGGGGTATTATTTAAAGCAGCACTTGCATGCCACAAGTTGGTGAATTAGATGTTTTGGGAAACTGGACATATGTATGAATGTGTGTATAGTATGAGAGATATCAACAGAGTATACTAAATATTTAACTGTGTAATGGTCATTACAAACCTAATTTATTGAGTTCTAATAGTTGGCTATAAATAATATTGAACCAAGTTAAATTATTATGTATATCTTCTCCTGAAGTTCTTATTTTATTTATAAAAGTATAAGCCCATTTATTAGACTTCTAGCTGATTCAATATACCACTGATAAAATTTGCAGTAACACAAAATATTTTTGTAATCAAACATTTTCAGTTTAGTTAAAGATGATTGTTTTGTCATAACATTAAATTAAATAATCACTTTCTCTGCACCTTGCTAGACAAGGATTTTTCTAGCTCTCAGGCCTGCCTAATTTCATATCAAGGGGTTTTATGCTTTTCAGTGTTTATTTGTAAGTCATATATGGTTTGCCTACTAACAGAAGATAGAATTATGATATGGGAGCCCAGCTGGGTGATGAAAGTTGGGTACTGTTCAATTAATATATTATGGGATCAAAGAGATGTCATTAAGTATCTTAAAGATGGATTTCTCTCAGATGTCTAATAATATAATAATATTGTTGTATGGTAAGATGCTTTAGAGAGGATAAATGGTTTTCTTATGAACAGCTATGGTTCACAGTTATATATTCTAATTGTATATTCTGATCATAATCATGATTTCTGTGTTTACTTTATTGCAG
Seq C2 exon
GGAATGGAATCTGTAGCTGTGGAAACTGTGAATGCTGGGATGGATGGAATGGAAATGCATGTGAAATCTGGCTTGGTACCGAATATCCTTAATGATGCCAAGGGAGACAACTGGATTCTTATTTCTAGGCCATTTTAGAAATTCAGAGGAAAGCATGTTACACAGCACTAGGACAGACTTTTGTGTATTTTTCTATTTCTGACTGCCCAAGTGAAGCATGGGTCTTCATTAGAAATGAATTTAGCAAACTGATGTAAGTTACACCATAAAGAATTGTTCTCCCATGACTAATATCAGTGTTTCACAACTGAAGAGGACAATTTTGTAACGCACAAGACAATTGGTGGTGTCTACAGAGAATTTGGTTGTCAGACTTGGTAGGTAGGAGTATTTGTGTTATGGGAATATTAGAGGTAGTGACCACAGACAATGCTGAACACCCTACAGAACATAGAAAGGCCCTTACAACAAAGTATTTTCTGACATCCAATGTTTAACAAGATGTAGTAGAAAAATGCTAAGTCTCATGGTATTTTGTACTCCACATCCCAAAACCAGAAACACTGTATCAGAATATAAGGATAATATTTATTCTCACATAAACCAACCAGTCAGATTTTTCCAGGATTCCATATGACTCTGAAATTGTATATGGAATGATAATGACAGACACATATGAGGTGTAATGATGTAGGCTGGGGGCTTACCAGATCACAAGGGCTTTAAACTCACAAGAATCTCTTACAGGAAGAAATGAAAAATGCACAATTTGACATTTTAATAAATAATGACATAAGTTGTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004516:ENSRNOT00000006264:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079748=EGF_2=PU(32.3=25.6)
A:
NA
C2:
PF079748=EGF_2=PD(64.5=64.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACGACGGTCTCATTTGCA
R:
TGTCCTCTTCAGTTGTGAAACACT
Band lengths:
343-1443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]