RnoINT0040274 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114444070-114446772:-
Coord C1 exon
chr8:114446176-114446772
Coord A exon
chr8:114444691-114446175
Coord C2 exon
chr8:114444070-114444690
Length
1485 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
ATTTCTTTCTCCCCACACAGCTT
3' ss Score
9.27
Exon sequences
Seq C1 exon
GCCCCGAGTACGCAGATGTGGTTTTTCTGGTGGACAGTTCCGATCACCTAGGGATGAAGTCCTTTCCTCTTGTGAAAACTTTCATCCAAAAGCTAGTCAGCAGCCTCCCCGTAGAGGCCAACAAGTACCGTGTGGCCCTGGCCCAGTACAGTGATGCTCTCCACAATGAGTTCCACCTAGGCGCCTTCAAGAACAGGAACCCCATGCTGAACCACCTCAAGAAGAACTTCGGGTTCATCGGCGGCTCCCTGAAGATTGGGAACGCCCTGCAGGAGGCTCACAGGACCTATTTCTCTGCTCCCACAAACGGAAGAGACAAGAAACAGTTCCCCCCAATCCTGGTGGTGCTGGCTTCAGCGGAGTCCGAGGATGACGTAGAAGAGGCTTCGAAGGCCCTGCGGGAAGATGGGGTGAAAATCATCTCTGTGGGGGTGCAGAAGGCTTCTGAGGAAGACCTGAAGGCCATGGCCACCTCTCAGTTTCATTTCAACCTCAGGACTGCCAGAGACCTCAGCATGTTTGCCCCAAACATGACACAGATCATCAAGGATGTGACTCAGTACAGGGAAGCAATGACTGATGACATTATTGTAGAAG
Seq A exon
GTGGGTGTCCTAATTTTCTTTCTTTTTTTTTTTTTCAGAGCTAAGGTAATTTTCTTTATATTGTTGTGATAAGATACTGGCCAAAAGCAACATAGGAAGCGAAAAGGGCTTATTTTAGCTTACAAGTTAACAGCCCATTGTAGAGGGATGCTAGGACGCAGATTCAATCAAGAACTGAAGTAGAGACCATGGTAGGACATTGCTTGCTAGCTGGCTCCCTCTAGCTTACTCATCTACCTTTCTTATATACTCGCACTTGCCTAGGGATGGTGTTGCCCACAGTGGACCGAGTCCTCTTCCCATCAATTAGCAATCAAGGAAAGGCTCCAGAGACATGCCCACAGTAGTTCTTCAAAGTGTGTCAAATTGATAACGAGATTTACCAGGACAGTGAACTGAGGCTCTGTGTATAGGACCACTGTCAAAATGATTTTGAAAAATCAAGGTGGGACGAGAATTAAAGTCCTGTGAATTCCCCTTTCTTCCAATGGGTAGTTTCTATCTCTGCTGTTTAAGAAGATATAGAGATTGTGGCAAAAAAAAAAAAAAGAAAAGAAAAAAGAAAAGAAAGGGGGGGTGCAGAGGTGGCGGGGGGGGGATCCCACAGGCCTTGGGTTTTTCATGGCCTGTTAAGTCCTGGATTTAAAAATTCTCCAGTGCCTTCTCATTTCCACCCAGGTTGCTCTCCACCACCTCCCTGGGTTTGTTCTTGCTGCAGGTTTATTACTGGTTCAGCGAAAACCAATTTGGTTCTGGAGAAACCTTTAGCTTTGGGAACCACACAGTGTAACTGCAGAATGTCAAGACTGAAGCCAACCTCTGGTTATTCAAACCCTATTGTGGAGCTAAGAATTGAAGTGGTATGATCTGCCCCAGTGCCAAGCAGTCACGTGTGGCCAGAGCCTGATGAAGTCCCCTGCTTTCTAGTTGGGTAGCCTGAACCCCGCATTGCTTATTCTGCTGTTTGATTCTGTGAATTAGCTCGTGTGTGCTCCACAGTCTGCCCCCTTGGATAAATCCGCTTGAGATGACCTACTGATAATACAGAATGCTTTCCTTGTGACAACGGATAGAAATGTGAACCATTACTGCTAGTGTCTTTCCCAAATAATTGAAAATGCAAGGGCACCCTTTAGCATTCCCTTTCAGTATTTAGGTTTGAGCTGCTGAGTTATAATAAAGGGAGTACCTGAAAGAGTTTCACATTTAATAGCTGGTGTTCATCGAATGAATTATGTCTATGAAGCTCCATGATAAGCATATTATCTATTTAATATCTATGCCAACTCTATGAGGTAAACACTACATCTCACTTCGTTATTTTATGAAATAATATATATATCTTATATATATTTACAAATAATCACATCAAACCTCTTTTACATAGCTGAGATCAAGTGTATGTTCTGTATGCCTTATGACACTCGGCAGAGGTGCAACCCTCCTGTGATAACTCTGCTGACTCATTTCTTTCTCCCCACACAG
Seq C2 exon
CTTGCCAAGGCCCATCTGTGGCCGATGTGGTATTCCTGTTGGATATGGCCATCAACGGCAGCCAAGAGAACCTAGATCATCTTAAAGCATTCCTGGGGGAAAGTGTCTCTGCCCTTGACATAAAGGAAAACTGCATGAGGGTTGGCCTGGTGGCCTATAGCAACGAAACAAGGGTGATCAGTTCTCTGAGCATGGGTGTCAACAAGACGGAGGTCTTACAGCGCATACAGGATCTGTCCCCTCACGTAGGGCAGGCCTACACAGGAGCTGCCCTCAGAAAGACGAGGAAGGAAGTCTTCAGTGCACAGAGGGGCAGTCGGAAGAACCAAGGGGTGCCTCAGATTGCTGTGCTGGTGACCCACAGAGCTTCAGATGACAACGTGACCAAGGCAGCTGTCAACCTCCGGCGGGAGGGAGTGACCGTCTTTACCATGGGCGTAGAGGGGGCTAACCCAGAACAGCTGGAGAAGATCGCATCCTACCCTGCCGAGCAGTTCACCTCCAAACTGAGCAACTTCTCTGAGCTGGCCACCCACAACCAGACGTTCCTGAAGAAGCTGAGGAACCAAATCACACACACAGTCTCTGTCTTCTCAGAACGGACTGAGACCCTCAAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.048
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=89.5)
A:
NA
C2:
PF0009223=VWA=WD(100=86.1)
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:
TTCAACCTCAGGACTGCCAGA
R:
GGACAGATCCTGTATGCGCTG
Band lengths:
351-1836
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]