RnoINT0040286 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114372834-114375975:-
Coord C1 exon
chr8:114375964-114375975
Coord A exon
chr8:114373328-114375963
Coord C2 exon
chr8:114372834-114373327
Length
2636 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TTTTTTCTTTTGTCTTTCAGGAA
3' ss Score
13.33
Exon sequences
Seq C1 exon
CTGTCAGACACG
Seq A exon
GTGAGTGATCTTCATCTACCTCACGCTTTACTCACGAAGACAAGATCGAGCCTGGTGATGAGAGAAACTGGACCTGGCCTTCCTTTGCTCACACTCAGAGCACTCGCGTGGGCTCTAAGGACTCAGCAGCTGTAGCTGAGTTTCACCCCCATTTCCCAATCCAACCAGAAGCCCGTTTGTTATGAAGCATAGGCTGATGACATGTATCATCATTCACCCACCCGACTTTTTAAAATATCCTTCCTCCCTCCTCCCGTTTTCTCTCTCATCTCTCCTTGGTCCTCTCCCAATCTCTCTTCCCACTCCACTTCTCCCTTTCTCTCCCGCCGCATCTCTGTCATGTCTCCTCCATGGTTCAGTGATGAGGATGCAGAGGGCAGAATGAGAATCAGGATCAGATAAAGTGAGAGAGATGTGCGGTGGAGATGATGCTGGGACCTAGGTAGCTCGTGCTTAATGGTAATCGCCAGCCTGCCTCAGTGACTTTTAATCTCGTTCTTTATGTGTTTTACCAATGCTTAATACTTGGCACATTTGTAACAGCCTAATATAGATATCTGGATACACACACACACACACACACACACACACACACACACACCCTTATTATATGAATTTCCCAGCCTTTGCCCTCTACTAACTCAGTCCTTTAGTAAGGATTTATCGAAAGCCTCCTGTGATCTTGTCTCTTGTTTTAAGCTGGGGACAGGGTTGACAGCAGACAAGATCCATCATACATTTCCACTCTTGTGGAGACTCCAGATAAACAAAGAGACGAATTCAGAATCTGAGATAGAGCCCAGGCAGCCTAGCAATGGAGTAATGTCAGGAGAGGGGTGGAGACTTTTTGGACCAGGGCTCCTCCCTGAAGCAGCGAACTCAGAGTCAGGACTAAAGGAGCCTCAGTTTTCTAAGTGTAAGGCAAGAAATCCAAATACCAGAGCTGTGAGCAGAGGAGTGGACATAGGCATTTCCCTAGAAAGCAACAGAGCCCAGTGTCCCCGCGATGCAGTGGTAGGAGAGATTAGCATGTTAAAAACAAATGAGGTAGAGCTAGAAGCTGCATCAGGCTGGGTAGGTGGACTCCATCCATAATGCCACACGGAAAGAAAGATCACTTGTTCTCCCTCACAGCCTGTCATATGTGTATAAGCGAAGGTAAGTGTGGGTGCAGCACACCATGTCGAGGGGCGAACAGGAAAGGGTAAATATCAGTGGTGAGGAAGGATGAGGTGCAGGTGAAGAGCCCAAGCCATGAAAGAGGAAGTAAAGCTGATTGCTTATCTAGGCTTCACCGTGTTGTAGACTCCTTAGGTTTTCTTGTGGGTAAGCAGATAAAAATGTACTCATCAGAGAGACTGTGAAATCCACTGTGGAGTGGCTGTTCTAGCTGTGTAAAAAGTTCACCCAGAAGTGTCAACTTTGGATCTGTTTAATCCCATAGTCGTTTATTTCAAGTAACTTTCGAATCACATCTCAATTACTGATAAGCCAGAGAATGAGTCCGATAGGGTGCGGGTAGGTAGATGGAGACGCCACCTGCCTGCTCTTAGGCAGAAGCCGTCAGCGCGAACTCTGCACTCTGCGGAGCCCTTGGGCTCCTGGAAACAGCATGCTGGGTTTGAGGCTTTGTTTCAAATTAGCCCTGAAGTGTTTTTTTTTTTCTTTGAAAACTAAAACTTTTTCTGTGTTTTCAGGCTGCACTGTTAACCCCTTCTTCCCTGTATCCCTAAATTATACCAGCGTCATTACTGGTTTTGTACCGTATACCAACAAACACAAAGCTAGAAGCATCAAGTCCACACTTAGTTAGGATTCACCTTTTAATTGTAAAATCAACATTCCCTTCATTTTTGAAAAAAATCTGCTCATCCCACTGATTAGACTCAGGGGCTAACAAATTATGTTCCCATCTCTGCTGAGATGAACGGATTTGGCATTAGCATGCACTATAACTGGCCATGGAGTTATTCCTTTTGTCTGTGGAACTCTAGTTCAGGATGACCTAGAACTTCTGGCCCTCCTGGCTCTACCATTCAAGTGTGTGGGTATAGGCATATGCTACTATATCTGTTTTCTGTGGTGCCGGGGATCAAACCCAGGGCTTTGCACAGGCCAGACGAGCAACACACTGACTATGCTATATCCCTAGTCTCTTAGCCTCCATTTTTTTTAATTATAAAAGAAGTCCTGACAGCCTTTAAAGTCCTTTCCCCCTTGTTTTTATCCTCATTAAATGAAAAGAATTTATGTTTCAACATGATTCAAGTACAGATGCAAACGACCATGCCTCTGAGCCAGCTTCTGCGGGGTTAAGGACACTTCCAAACAGGTTCTACCATTTAGAAGGGATTGGGTAATTAATTTACGAGCTTAGTCCCTAATCATGTTGATTTTAGACTGTTTTCTTTTCTGCTCATCCCAGCAGAGCATATAGCCAGCTTTTAAAACAGCCATTTTAACGACTCAAGATGTAAACATTTAATATTTTATATGTTTTAATATTTGGGTTATTAATTATTTAATGCTTAAATATTTGAGCAGTTAGCATTTAAAATGATTTTGCTTTCCATGTATTGGTTTTAGGCAAACATTCTACAGGACAGGAGGCATGTTTTTTTTCTTTTGTCTTTCAG
Seq C2 exon
GAAAACCTGAGTGCCCAGTGCATCCAACTGAGTTGGTGTTTGTCCTGGACCAGTCCCGGGATGTCACAGAACAGGACTTTGAGCGGATGAAGGGGATGATGGCCTCCTTAGTTAGGGACATCAAAGTTAGGGATGCCAGCTGCCCCGTGGGTGCCCGCGTTGCCATCCTAGCCTACAACTCCCACACCAGGCACCTCATCCGCTTCTCGGATGCCTACAGGAAGGACCAGCTGCTCAGGGAAATTAAAGCTCTTCCTTACGAGAAATCCTCCGACAGCAGGGAGATTGGCAAAGCCATGAGGTTTATCTCCAGGAATGTCTTCAAGAGAACCCTCCCAGGGGCTCACGTGAGAAGAATCGCCACGTTCTTTAGCAGTGGCCAGTCAGCCGATGTCCAGTCCATTACCACAGCTGCCATGGAGTTCAGTGCCCTGGACATCATACCAGTGGTGATTGCATTCAGCAACGTGCCCTCGGTCAAGCGTGCCTTTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:31
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=0.091
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(92.8=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
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]