RnoINT0039940 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112463779-112465464:-
Coord C1 exon
chrX:112465396-112465464
Coord A exon
chrX:112463815-112465395
Coord C2 exon
chrX:112463779-112463814
Length
1581 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTCTATTTTTATTTCTCAGGGG
3' ss Score
10.43
Exon sequences
Seq C1 exon
GGGCTGCCTGGTCACAAAGGTGCAAAAGGAGAACCTGCTTCTTTTCAAGGCAGCATCATAGGAATGAAG
Seq A exon
GTAAGAGATCATAAAGCAGGCAGCTGAGTGGGTGGGAAGCAAGGTTTCACAGAGCCAGGACCTACCTCACACTAGGCCACTTCCAGAACTAATAAACCTGTGCCGTTGCTTAAGGAACAGACCCAACTGATTTTAAAAGGATTCCAAGCCTTTTGGTGGTAAAAACATTAGCAGAAATGTCTGCAGCTATGCTGTCTAGAAATTTGTTTTCCAGGATCTGCACCAAAAATAAGAGAGAAGTTGGCATAGAGTTTGCATGTTTTTCTTTGACAAGCCAAAACATTTTCTAGAGGCATATACTTTTTTTGTTTCCTCTAAAGCCTTAATTCTTATGCATCTTGGTTTGAATCTGTATATAGTCTTATACAGCTTAGTATGACTACCACCCCAGCATCCAGGTCTCTCCTGTCTCTAGATTCCTGTCAACGCTAAACTGGAACCTGATCTATTGTCAATAATATTGTTTTATTGAGCCTTCGTCTATTTCTAATTGGTAGCTTTGTGTGTCTTCAGTAAAACCTGGTTTCAAATGATTGACCCTACTCCTCTATAGACTGGGAAAGAGTCCATCACTGCTCTCAAGGATAACAAATAGGAATGTATGTGCCTGCAAGCTAACTGAGATAATTGACACCACTCTCCCATCACTGCACAGGGCCAGGAACCTTAGAAACTGGCCATAAAAGTAGTGGTGGGGATGGAACATCTGGATAAGTGGAGAAGAAGCAAGGATATTTGGGTTCTTGACTGTGGATGCCATAGCAGAAGGTAGAACATTAAAGTTGGCAAGGGCCTCATGGTGTTTGGATTCATGTCGCTTATTAGACAGATTGAAAATCTAAGGCTATATGACTTACTCAGAGCCAGATGGCCAGTTCTCTGAAGAGCGAAACTTCAGGCAGTGTTCTTCCCATGCTACAGGGAGCTGAGAGGTTTTTACTGTAAACCAAGCAGTGCAAGACTAGCAGGTGTCAAAGCACAGCCATTGTCTTAGCAAAGGTTAATGAAATGGTTTTTCCAGAAATCAAAGAAACCTTGGATCCAGTGGAACACAGCAATTTCCACAAGATGGTTATATTACAGATTCATACAGTGGCTTAAGATGCCGCAAAGTAATTAAAATGTAATCAGAGTCTGTATGCTCTGTTGATTTTCCCTTGAAATGTCTGATTTGCATTGTATACATATAGGCACAGATTCTCTGGGGATGAAGGCACATGGGAAGGTAGCTTTGCTTTCCTCCAAAAAAAGAGCAGAAAATCACCGGTCTGCAGAAGTGTTTTCTAATGGATAAGTTCCTAGCAAATGTGAAAATTAATTAATCTAGGTAAAATAGGAAATCTTGTTCAGTCAAGGCTATAATGTTTGTTTTCTAGAGTCCAGAATGTTCACAGGGAAAAAGAAAATGGGTAGATACAGCCAATGTATGTATTATTTAAAACTCAAGACCATGAAAGAGGCCTAAGTTGCCTCAATTTGTTTCTATCCCCATGAATCTCAGGTTGGTTGTCTGAAACCCTGTGGTGGGCTTAGCTTAGTAATCTCTTCCGTATGTTGTTTATTTCTATTTTTATTTCTCAG
Seq C2 exon
GGGGATCCTGGGCTGCCTGGACTGCATGGAATCACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:4
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=PD(21.7=56.5),PF0139113=Collagen=PU(7.1=17.4)
A:
NA
C2:
PF0139113=Collagen=FE(19.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]