RnoINT0039924 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112429214-112431183:-
Coord C1 exon
chrX:112431022-112431183
Coord A exon
chrX:112429345-112431021
Coord C2 exon
chrX:112429214-112429344
Length
1677 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TCTCTCCTGTAACCATTCAGGGC
3' ss Score
8.09
Exon sequences
Seq C1 exon
GTTTGAGCGGGAAATCTGGTATGCTAGGCCCCAAGGGTGAGCGAGGGAACCCTGGAACATCAGGACCACCAGGACAGCCGGGACCCTCAGGGTCTACTGATCCATTTGGTATCAAGGGCACATCTGGACTCCCAGGAGCACCAGGCCTTCCAGGCATTTCAG
Seq A exon
GTAAATCCATTGAAGGATGAATCCCAACCTGACAGACTTTAGTTAGGCCTTTAGCTAAGGCATCCTGGGGACTAAGAGTGACAGAATGACATGCTCAGCATGTAGGGTATTTGACTTCTCTAACCTCTCTAGTTTCAAATCCCAGATCACCCTGGCTAGGCCAGACCAAAACACATTGCTACTGTTTAGCTTTTGAACCATGACAACAAATCTCTGTCACTTCCCTGTTCCAGGGCCTCCTATCCCCCTTTGATGCTTTGGTCTGCCTCTGGCCTTTTTCTATTAAAGAAACCACCCCGTGTTGAATTGTGTTAAACCCTCACTGTGGCTGTGTTAAGCCTGCTTTGAGCTACAGAGAAGCTGGAGCTAAGTGTGACCCCTCCCCTCCTCTCCCTCCTCTCCCTCCCTTTCCCTCACCCCATCAGCGGCCTACCTGTAAGGAAAACAGGCTTCTGAGAGTCCATGAGCAAAGAGTGGCTTTCCACTCAGTATCGGGGACTGACACGCACTGGTTCCAGCCTAACATTTGCAGATCACCTTTTGTTTGTCTGTTTACATCATCACCCTTACTCTGCTGCCTAGATTGCATCACTGACCGAGTGACTGAAGCTGGGTTATTGGCAGAGCCCATTAATATCCCTTTTATTTTCTTCATCCTTCTGTTTCTGGCTTCTTGATATAAGTTGCTGAAGTGAAGGTCAAAAAAGAAAAAAACCCACAAGCTCACTGACTAAGACTCCCCACTGGGGAGTTATGTGATTATCTACTCTAACATGGCCTTCCTTACAAGGGATCCCTGGATCCCTGAACCCCTGCTATAAGGTTCGTTCCCATTGTATTCCCTCTCTTGTTGTAGAGTTACCTTCATAGCTTCCCATTGGAGTCCTGGGGCTCACAGTTACTTGATGTTTTTCATTTTGTAGAAAGCTATGTCAGCCATTCATTGAGATCCTTGGGAGCCCAAATACTTCTGTCGTCACTGATTTAATCCTTTGGCTTTTTCATTTCCTTGCTTTGTACCTAGACATTCAACTTTAGCAGCAACTCAGGAGGTTAATCCCATTGACCAACTTCAAGCCCTGGTGAAAGAAGACTCAGAATACCTAGGAGACCAAATGGGCCTTGTGGGCTTCTACAATACTTGGCACTAGGGGGTCTTTCAAACCTAATGCCAAGGAACTGGCTGATTTAACTGCTTGTTTGGGGGATTAAAGGGGCAGCCCTGTATGCAAGACTCCCCGGGAAGCCAGAACAACAGCAGTTCAGATTTAAGGAATTGGCTCAGGAAACAACCATTGTAACTTGATTCAGGGTAGAAGTACCAGGGAAATTGGAGCCCAATTGTCACCCTGCTCTCCTAGAGCTCCATTTAGCGGCCCCTATGTGAACCACATTCATAAAGGGAGAAATTATAATTACAAGGTGGTTGCTTTTCCTGACCACCACTGTGCCATGCTGGAAGTGACGAGCATTTAGGGTGGTGCTCTGGGTGTGTAGGTACTAATGCTCAGACAAACTCAGCACTGGGCTTCTTGGCACCTCTCTTTGGGTATTGTTAAAGGACTGTGGACAGACCCCTACTAGCCAGCCAATTAGAACCTGTGGGAATAAACAGTGATCCAAATCTGACCAGAGTCTCACTAGCTGACCTGTGTTCTCTCTCCTGTAACCATTCAG
Seq C2 exon
GGCACCCTGGAAAGAAGGGCCAAAGAGGAGACATAGGTCACCCTGGGTCAACTGGAAAACGAGGTCTCCCTGGAATAAAAGGCCTTCCTGGTCCTCAAGGGTTAGCTGGCTTCCTGGGGAGCCCAGGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:24
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(49.2=58.2)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=22.7)
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:
TGAGCGGGAAATCTGGTATGC
R:
CTCCCCAGGAAGCCAGCTAA
Band lengths:
280-1957
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]