RnoINT0040288 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114363036-114366552:-
Coord C1 exon
chr8:114366456-114366552
Coord A exon
chr8:114363705-114366455
Coord C2 exon
chr8:114363036-114363704
Length
2751 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
CTGAGTGACTTTGTTTGCAGACC
3' ss Score
6.69
Exon sequences
Seq C1 exon
ATTGATGACACTGGTACATTCCAAGTCCTTGTGGTTCCCTCCAGGCCTGACCAAGTGCCAGCGTTAGAGAGACTCCAGCGGTGCACTTTCTGCTATG
Seq A exon
GTGAGACCCACAGGGAGAAGTGAATTTGATCGGGCCTCAGTGCGTTGAGTCACCATTGGCAAGAGCAGCTGGAGCTTGGCCATAGGGATAGGCATGGCCTAGGGCAGACCTCGGGACGCACACTAGCTCTTCCACACATGGAGCCTCTCAGCTCAGCCTGCAGGGCCCTTCCGATGCACCCCAGCAGGAAGACTCTCCTCCTCTACTTTAGTGCAGCTTCCAGGAAACAATAATAATTGAAAAACAAAACAAAAGCCTTAGCCTGTCTCCTTGACACACAGACACACACACACACACACACAGACACACACACACACACACACACACACACACACACACACACACACACACACATACACCTGGCCCCAAAGGCTTTGGAGCAACCTGGCACCTTCCTGGTTGGGGAATTATTTTTCAGTGCAGTAGGAGTTGAAAACAAACTCATACATCCTCGTTCAGGAGTCTTCACAGACTCCCAAGAGTTAGGCAACAAAAGGATTCGCAGTATCGATTGTGGTGCAGCCTGTTGCTCTAGCTGGAAACAGTCTCTCTCGTCTTCTGTCTGATGTTCCGTTGGGGTTGTAGGTGGTCATGACAGCGGGCAGTTACCCCGTTTCTGCTACAGTCTGTGCACTGTTTGATGCCAACTACTGTGGTGACAGTTCAGGCTTAAGCTATTGGGATCCTTAGGTTCTAAGCACGGGTTTAATTGGTTTATGTAAATTGTGTCAACCTTATAACCACACTGGAATGTTTGAACTATTATTAGTAATATTGTACAGATGAGGGAGGTCGAATTGAGAGAGATGTGGTATTTTCCTCAGGGTCCCACAACCAGATCAAACCCAGGAAAGCTGGTTCCGAAGTGCTTTTAATTTTTGTTGAATAAGAGTCTCCTTCTGTTCCCTGAAACCCACCATTTAGACCTGGAGAAAGACAGTATGATGCCATTTCCATGTGTACCAGTGGAATGCTGGGGTTTGCTATGTAGATGACCTCACATGGAGAGAGGGATTCTGAGAAGGGGGCAGACAGTTCCTTTTCTGTGCCCCTCTACAGCCCTGGATTCAAGCTTTGTGCACGCACCCTCCACTCCTGTGGATTGTACTGGGAATTCTGGGATCCCGGTTCTCTCCCTCACAAAAACTGGTGAAGTGCTAAGATTCAGTCTGTCTGCTCTTAGTTGCGACCCTGGACACGTCAGCTCCAACAGTGTGCTGATGTGTTGCAGTCGGTAACTGCACATACGTGACTAGGGATAGACTTTTGGCTCTGTGCCTTGGCTTAAACCCTTGTTTTGTCTCACAGGCATATAATGGAAGATATTTTGGCTGTCATTTCCTGCAATTAAAAACCCCACAAAACAGAGCAAATGGGCAGCCTGCTGTCCCTGATTAAAGAAACAGCTCTGCACACAGGTGACTATTCCGTCATCTGACCATTATTCAGGGTTATAAAATTTCACTAAACTTCAGTAAGGGACTTAGGCAGAGCCATCTTTATTGAGTCCATGAGCAAGCAAGAAGATAAGAAGTTTGCTGCACCCACACAATCACATGCTAGTCATTAGCGCTTTCACTTAATAGTTGGTATTTATGGTCCATGCTGATAGCTAAATTCTATCTGTATGCTTGTTACTCCTCCTCTCATTTACTAACAAACTAGGCAGACCCTAGCATCTGGGTCAGCCTGATTCCCAGTTAGTGACAAGCAATTAGTTGTACAGAGAAATTGTACGCTGAGGCCTAGCAGTGACTTATTCAGAGGTGACATGTTCCTTATGTGATAAAACCAGAGCTGGGCATCCCAGCTCTCAGGTGAAGGGGCCACCCTGCGATCTCATGTGTGCTTATCTCTAACAATAAGACACTGCAAGCTAGCTCAGCAGGTAAAGGGGCACGTCCCCAGACATGACGACTTGAGTTCACTCCCAGGACTCGTGCAGAAAGAGGAAGCTTGCTCTTGAAAAATCCTCCTCTGCCTCTACACACGTGCTGGGCTATGTGTACCCATGTGTATAACAGATAAGTAAATGTTAAAAAGGAAACACCACTGACTTCATATACAGAAACTTCTAGAAATATGGTGCATCCATTGTGAACGACTTTACTTCCCTGCCTCAGCGGGTTCTATGAAAATAGATTAAGTGAATTCTAGAATCCTCCCACTTCTGATTTATCATATTTCCCCATTCATTCACTGTGGTCACATTCAATAAAATCTACTCTGTTTTTCCTTGCTATGCATGCATAATGCACATTTATAAAAATGACTTTGCTTTATGGAGGAGCATTTTTTATAAGGGGCCCAAAGTTGTGAACTCTTACTTAAATTGAAATAGAATACGCATTGCCTTTTAAAGCTTACTGTTTAAAGCAGATGAATTTTTCACAGTTAGTGTAGTGATTAAGGCCCTGGGTTTAGCCTGTACACAATCGACACTAGAAGTGTGTTCTCTTATAGTGTGTTCTTACGTCGGGAGATGAATTGCTCAAACTTTGTAAGCACAACCGTCAAGGTTAAACTTCCACCGAACACAGCTTAAAAACTGGTAACGTGGACTAGAGTCAAGGACTCATGGGCTGGCATCAGATCTGGACATTTTGGTGATAAACTCTTACTCTTGACATTGTCAGAGGTGTAACTATTTTATGAGCAAAGTCTATGTAGTCCCTACATGCTAAAATAGATGAGGCAGAATCTTTCCACTTCCTGTCTCTGCTTAGTAACTCTGAGTGACTTTGTTTGCAG
Seq C2 exon
ACCTATGCAAGCCAGATGCTTCTTGTGACCAAGCCAAACCCCCCATTCAGTCCTACCTGGATGCTGCATTCCTGCTGGATAGCTCCTGGCATGTGGGAGGTGCAGAATTTGAAGACATGAGAGACCTCCTGGAGGCCCTGCTAGATCACTTTGAAATCGCTTCAGAGCCAGAGACGTCTGTCACTGGAGACAGGGTGGCCCTACTGAGTCATGCTCCCGTTGACTTCCTACCCAACACCCAGAGGAGTCCCGTTAGAACTGAGTTCAACCTAACCACCTATAGCAGTAAGCACCTCATGAAGAGACACGTGGAGCAAGCAGTCCAGCAGCTGAATGGAGATGCTTTCCTTGGTCATGCCCTCAGGTGGGCACTGGACAATGTCTTTCTAAACACGCCCAATCTGAGAAGGAACAAAGTCATATTTGTGATATCTGCTGGGGAAACCAGCCACCTGGATGCGGAAACCTTAAAGAAAGAGTCCCTGCGAGCCAAATGTCATGGGTATGCCCTCTTTGTGTTTTCCTTGGGCCCTGACTGGGATGACAAAGAACTGGAAGACCTGGCCAGCCACCCACTTGACCAGCACTTGATCCAGCTTGGCCGAATTCATAAACCTGACCACGGATATGGTGTAAAGTTTGTGAAGTCCTTTATAAACTCCATCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.009
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(6.0=30.3)
A:
NA
C2:
PF0009223=VWA=WD(100=80.8)
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]