RnoINT0039938 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112411558-112413610:-
Coord C1 exon
chrX:112413512-112413610
Coord A exon
chrX:112411705-112413511
Coord C2 exon
chrX:112411558-112411704
Length
1807 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTTTCACCACCCGCCCTCAGGCT
3' ss Score
6.59
Exon sequences
Seq C1 exon
GCATGAGAGGGGAACCTGGCCTCATGGGGACTCCTGGCAAGATTGGGCCACCAGGAGACCCAGGATTTCCTGGAATGAAGGGGAAGGCGGGGCCAAGAG
Seq A exon
GTGAGTGCAGGGCCAAGCCTGAGCTGTGGAATAAAGGGGTACAACATGAAGTTGGGGTTCTTTGGGAAGCCACATTGTCTACCACACCACAAAACCAACTAGGGCATCCCAAACCCAGGAGGTAGGTTCTCTCCTCTGGAGATACCTCTGTGCCAATCTACTCCCAGAACTGAGGTCCTTACTGCTTTGCTACCATGGGTCCTGCCTTCCCTCTGAATTACTTCTGCATTTCACCTAGACCACTAACCTCATTTTCTTCGTTCAGAAAAGAAGCAAAATTCTCTCTATCCATTCAACTATTCGGTCTATCAGCAGCCCCTGAGGTCTCCCTCTTCTAGCATGCCTAGCATCTGTGTACTTCCCATCAGTTCTGCTGTGCCTTTGAGGTCTAAGCCATCAACGTTTCTCATGTAGCAGCCTTCCTCCCCCAAAGACAATTTTTTCATGTATAGTTACTGACAAAAGGCAAACCATTCTATTCATGGCATGGAAAAGAACCATAGCCCACAAAATAATATATGACACCTCCCTCTGTCCTCATGCCAACCTGTCCTTTTTACTGTCCACATTGGCATCTCAAATATTGTCCCAATTACCTTTTTTGTCCTCTTATCCCCATCCTATTAGTTCCCTCTCCCCTAATTAATCACTCCTATGTTTTTTTGTCATATATGTTCACGTGACATGGTGCTCTCCAATTGTATTCATTTGCTTGTACATGATATGCTTCACTTTTCACCTGACTGAAGAAAGTTCCTTCCTGTATATGTGTCCCATTTTATTTGTCCATTCATCTGTTAATGGACACTTAGGCTGTTTCCAACCCTTGACTATTATGAATACTATAGGGATTAACATAAATTGTGGTATCTCTATGGTATGCTGACTTGGAGTCCTGTGAGTACATTACTGAGAATTGTACTGTTGGATCATATTTCAATTCTAGTTTTAGGGTTTATTTTGAGGAGCCCCAATATTGATTTCCACGATACCAATACTACATTCCTGTCAATACTGTATATGTTTCATAATGCTCTCTTATCCTTCAATTCTTTAAATGTCTAGCTCCCCCTGATACTTCTGATAGTTGAATAGTGTCAGCATAACTGTCACTGGTTATAAGAAGCCACTGGTAACTCTAAAGCAGATCCCTCTACCCAAGTTACCATGCTCCCTCTCATTGTCACTACATCAATTATTTCCTTCCCAGTCCTTCTTAAGATGTGCACAACGGGGTTAACGATATTTGCCAAACTTTGCTTTGCTCATCTTCATCACTAATCCATAGTCTCCATAAAGGTCCATCACTGCTCTTGTTCCTCATCTCCCAGAATCTTGAAAGATAGTAAGGACCTAAGAATTACTTGATTAATGAATTCGTAAACAAGCTATTCTATTTCTAAAGTGGCTGACTTGGGTAGGTCTTTTAGGCTGGGATACCAACTGCATCTCTGGTGCATTCTGACCAGTGTGTAAGTAAATATCTGTTCCATCCCTAAGCCAAGGCTATTTGCAGCAGACATTTCCTAACTGCCTTCCACCATACTGAACTATGGGGGTGGGGTTCCAGGGGACAATAAGTATGATTTGCTCCCTGCCTTGACCACATGAACCCACCAAGTCACTAAGAAGGAGATGGGGAAAGAAGGTTCTATCAAGAGTTCTGTATTCTGTATTGGAAGCCTCAAGTGGGAATTGCGAGCACAAAAAGAAAGAGAAAATAGTTGGTGATTGCCAGGTAGAGGGAAGGATGCCTTATTCCTCTCTGTTCCAGACTAACCTGTATTGTTTCACCACCCGCCCTCAG
Seq C2 exon
GCTTTTCTGGCCCCCAGGGTGCTCCAGGACACACACCAATTGCTGAAGCTCGGCACGTTCCTCCAGGACCTTTGGGTCTGCCAGGCATTGATGGCATCCCAGGCCTCACAGGAGACCCTGGATCTCAAGGCTCTGTGGGTCTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(55.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(18.3=22.0),PF0139113=Collagen=PU(54.2=64.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCTGGCCTCATGGGGA
R:
CAGACCCACAGAGCCTTGAGA
Band lengths:
231-2038
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]