RnoINT0040207 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114701298-114704018:-
Coord C1 exon
chr8:114703968-114704018
Coord A exon
chr8:114701334-114703967
Coord C2 exon
chr8:114701298-114701333
Length
2634 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTTATTGTCTCTGACCCTAGGGT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GGTCGCTTTGGTCTAGACGGCTACGGTCATCCTGGAAGAAAAGGCAAGAAG
Seq A exon
GTGAGTTCCTGCAAAGAGCATTCCAATCTCAGGTCACGCTTTGAGTTCTACTAGACTATAGTGACTTTTGAAGAGGTATGCCAGGGATGATTTTTATGACATGACGCACATAGCGTGATAGAATTCTCTCCCTGAGAAGTAAAGGGCTGGTCTCATCCTTCACTTTCCTGCCTTTACCCCTTCACATGCATGCTCTACACTTACAAGCTCCCAGTGATGGATCCAACCAGCTGCAGGTTAAGACATCTGGGAAAATCTGCATGTGTATAGAACATGTATGAATTCTTGTTATCCCCCTAAATAACACAAGACGATGATGCCTGTTCCATAGCACCTGTAGTTGTAGGTATTGTGTCACCTGGAGACTGAAGTCTAACAGAGGGTGTGCACATGTCACATGTGTGTACTGGGTGGCACCGTATTACATCAGGGTGTTGACTGTGCTCAGATTTCAGTACCTCCGGAGGAAACCGGAACCAACCTTCCGAAGATATTGAGGGGCGATGTAATCCTTTATTTCTTTTAAAAATACATAATATTTTAACTTTTTCTTTAAGAATCTCATATTCTGGTTTCATTCCCTCCTCCCATTTCCCCACTCCAGCTCTTCGAAGATCTCCTTCCAACCTCTGTCTCCTTTTCCTTTCAAGTCTTTAAAACTTACTAAGTCTGTTTATCCTGGCCCATACGTATGTGGGAGCATCTACTGGAGCACGGGACCTCTACTGAAATTGTAATTTCTAGGTGGTGGTGGTGGTAATTGTAAAAACTATTTAGGAATTGAGGACCCCTGGTATTGAAATGTGGTCTCTTAGTGACCTTCTTTCCCAGAGGGATGTTGAAGAAAAACGTAATCGCCTGGCACTGAATGTTATAGAAACATGTTCAATATAGAGAGAGCTGTATTCCTAAAGAAAACTTGTTTTCCTTCTAGTGGCCAGCAACTTAATAATTCCTCAGCTGGGGTGGGACTTGTGCCACTTCTCAACACACACTGTTGTAGTGCCAGGGAAGTGTTAGTGAACACCCTGCCTCCCCCAATAGACAGGATGCAAGGCAAATCACAGCAGGGCCTTTATCTCGGGCCCTTAGCCCACTGCCAATAGGTAGGATGGTTTTGGTGGAGTGGAGCCCCGAATATCTATGTGGTGAAGTTTTATAGAAAGCAGCAAGTCAGAGGTGGGGTGTTTTTAGATTGGCAAGCATCTAATGAGGTGGCTACTGTGATCTCCAGTATAATTGGCTGGTGCTGGGGGGTAAAACCATAAACATAACTTCTGCTTCCCTCTGCATTGGTGGTTGTTAGGCAGGGGGCAGGGCTGGTTGGCAATTAACTTGAAAACCCTGGATTGTTGGGAGAAACTAACCTAGAAACGCTGGTCTGTTGGGATTAGCCTAGAAACTGGCTAGGCTCAGGTTTGGTGTGGGGTAATTTGGAAACTAATGCTAGGTACTGGCCTGTTAGTTCATCTGAGTTCAAGTTTTCTAAAATGGAGTTTGAACCTAAAAGATTTGGTCTCTCACTATAACCTTTATTTATTCGTGTGTGCACACAAGCACTGTGCCATGTGTGTGCATAGGAGGGAGGACTGCTTGCTAGGTTACTTTTCTCTCTTTACCACCTTTGGTTCAGGGATTGAACTTGGGTCGGCAAGCTTGGTGGTGAGCGTCTTTCCCTCACAGGACCATCTCACCAGCTCATTTTTTCATTTCCTGGTCCTCTCTCTGGATTCTTGGTCCATCTCTGAGATGCTGTCTACTTCTATGGTCACTTGCTTCTTCAGGAATGCAAATTCTGGGGTGGGGGTCTTGGTTTTGTGTACTGCTGAGTCTCCAGTGATTACAGGACCACTTGGCAAACAGCAAGAGCTAAATAAATGCCTGTGGGATGCATGATCATTTTGAAGCATGTCTATGGCTCTGACAAGTCGATGCTGCTTCCTAACACTCAGGTTGATGCCCCTACCTTGCTTTCTGTTGGCGCAGATCTCGGGGGCTCTACCCTGAGAAATAAAAATGCCCAAGAAGGAAGTTTCATTAGACTCTGCATCAGAGATGCTGAAGATTGTAAAAACTATAAATTGTTGATCTCTGGAATTAAAATGCAGCCTCTTGACAACAGTTTCTTCTTTCCCGGAGGAATGTCGAGGTAAGACTTAATCACCTGGCACTGAACATTATCTTATTGTCTCTGACCCTAGGGTGAACCTGGATTCCCTGGCTATCCTGGCTTGCAAGTAAGAAGAGATCTCCGTGGGCCTGGCAACTGGTAGGCAAGTGTGTCACCTGTGTGCAATTCTTTCTTCACATTCACAACCCTGCTTTTGCCTTTAAGGGAGAAGATGGTAATCCAGGCCGTGGAGGAGAGAAGGGGGCCAAGGGAATCCGAGGGAAGAGGGTAAGAACCGAAGGGTCATCTGCAGTCATCACAGAGGCTGACAGGGCTAGACTATCCTTGACCAGTCAGTCATTAGACTCTGCATCAGAGATGCTGAAGATTGTAAAAACTATAAATTGTTGATCTCTGGAATTAAAATGCAGCCTCTTGACAACAGTTTCTTCTTTCCCGGAGGAATGTCGAGGTAAGACTTAATCACCTGGCACTGAACATTATCTTATTGTCTCTGACCCTAG
Seq C2 exon
GGTGAACCTGGATTCCCTGGCTATCCTGGCTTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:25
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=PU(10.8=47.1)
A:
NA
C2:
PF0139113=Collagen=FE(14.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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]