RnoINT0040289 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114360031-114363704:-
Coord C1 exon
chr8:114363036-114363704
Coord A exon
chr8:114360125-114363035
Coord C2 exon
chr8:114360031-114360124
Length
2911 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
AGAGCCTATTCTCTTTCTAGATG
3' ss Score
7.95
Exon sequences
Seq C1 exon
ACCTATGCAAGCCAGATGCTTCTTGTGACCAAGCCAAACCCCCCATTCAGTCCTACCTGGATGCTGCATTCCTGCTGGATAGCTCCTGGCATGTGGGAGGTGCAGAATTTGAAGACATGAGAGACCTCCTGGAGGCCCTGCTAGATCACTTTGAAATCGCTTCAGAGCCAGAGACGTCTGTCACTGGAGACAGGGTGGCCCTACTGAGTCATGCTCCCGTTGACTTCCTACCCAACACCCAGAGGAGTCCCGTTAGAACTGAGTTCAACCTAACCACCTATAGCAGTAAGCACCTCATGAAGAGACACGTGGAGCAAGCAGTCCAGCAGCTGAATGGAGATGCTTTCCTTGGTCATGCCCTCAGGTGGGCACTGGACAATGTCTTTCTAAACACGCCCAATCTGAGAAGGAACAAAGTCATATTTGTGATATCTGCTGGGGAAACCAGCCACCTGGATGCGGAAACCTTAAAGAAAGAGTCCCTGCGAGCCAAATGTCATGGGTATGCCCTCTTTGTGTTTTCCTTGGGCCCTGACTGGGATGACAAAGAACTGGAAGACCTGGCCAGCCACCCACTTGACCAGCACTTGATCCAGCTTGGCCGAATTCATAAACCTGACCACGGATATGGTGTAAAGTTTGTGAAGTCCTTTATAAACTCCATCAGGC
Seq A exon
GTAAGTCATAAAACCGTTCCTGTGTGTAAGAGTCTGCTCGGTGTTCCCTAGAAGGGCCATGTGCTGTCACGCCTTCCTGGACACCTCTTGCTTGTCTTCAAGGGCATTATGGGGTCAGAGAGGAAAATATGCAATAATGGACACCGGAAGGGAGGACACTCCGGTTCCTACGCAGTTAATTTTCTGGCTCATCCTTTTTTAATACCTCTGGTTCCTATGGAGAAGCAATCATAACAAGCAGCTGTCCACACATCTGTCTGCATGGAGAAGTGTAGTCTAGGGGTGTGAAATCACAGCCCGGGCTCGGGCTCCAGGGCAGAACCCTTGCCAGGTAACACTAGCACACTGCCCTTTGGAGAGAGGCTTCTACAGTTAACACACAGAAAGAGCAGCCAGAAAGAGAAAAAACAAAAAACAAAAACAACCCAGAAACAGTCCTTGGCTTTGCTTTGACGAATTCCGAAGTCTGAGCTGAGAATGTTGGGCGGTACCATTTTATTGGTTAGAATGAAAGGCATGGCTTTGCACAACTTTCTCTCAGTTCCATGACCTCGTAGGAGCCACTAGCAAGAAGAAATGGTGTCTGTAAGGAGACAAACCTGGGCTGTTTGTCTTGCAATGGGCGCCCTGAGCAACAATGCGGTCCATTTTGGATGCAGCAGGATGGCCGAGGAGCCTTGCCCATATTCGAGGCTGAAGGGGGAGGCGCGGTGGGAAACTATCTGTTCTCAGAGCCTGCTGCCTCTTGTCTGAGGGAGTGCAGATGAAGAAGCAGGAAGGCACAGGCAGAAGAAGGCGTGAGGGAGTGCCTGGCTAGTTCTTAAAACTGTCATTGAGGAGCGAAGTAAGTTGAGGCTGGAGATGTACTGAGCGGTGCAGAGAGACTGCTGGTGGGGGCGAGGGTAGGCAAGGTCAAATCCTACTCAGAATGAGTCTAGGACCAACACCAGCTGGGGCTGGTTAGACACCCAGGGTTCAGCCCCACCCTAGACATTCTGAATCAGAATATGTATCCTACCAGAGCTCCCAGGAAACCCACATACAAGAAGGTTTTGGAAACACGGGTGTGGGAGTAGTGAGCCCCCCGAGAGTGAGATTTATTTCCATAGATCTGGAACAGAAACCTCAGAGAGGAGCTAAGGGCAAGGGGTCACCCTGAAAGAAGCTTGTTGTAAGGGTTAAACAGAAGACCACTTGGTAAGTCTTTGGTAAACTCAAAAGAAACATGCTTGATGGCCCACAAGGCTGGGGGCAAGACTTGCCCTGAGGTTTCCTTCCTGGTATCCCATATTTCTTCCTGCCGCTCATGCCAGGGCATCCAGCCACGTGATCTAATGAGGCAGCTCCTCCCTCTTAGGAAGAAAGCAGAAATGTTTTAAGCAAAGAGCAGGTAGGACTCAGGGGAGATAAAGTGCCCTGACGTATGAGCATGACGCAGCTGCCTGCCCCATTTCCAAAGCTGTGACACCTAGAAAGCGCCATCTTTAAAATACAGCTGTAAAACTGCAGGAAGTCACTCCTTCCACAGGCCCGCATGGTCATGCCCACTCAACTGGGCCTCTACTCTGAGCCACTGACTGCACAGGTATCAGGCTTAAGGAGTAGACTTGGCCAGGTCCCCTCTGACGCTTCAGAAGCCTCTCAAGTGTTTGTGAGTCATTTGGTACACTGCCACAAAGTGGACAGCAGAACTTGGTCCACTTCAGAGCTGCACGTCCCCTAAAGGAAGCCAAGCTGCTGAATCAGCAAGCTTCCTACGCCCTGCTCAAGCGGGAAAAGGAAACCCAAAGCCAGATCTGGCAGGCGCAGCACACACCTGGAATTTTGGTTTTGGAGAGGCAGAGAGGCAGGAGGATTGCTGCAAACCCAAGACGAGACCAAGCCACCTAGTAAAACTACCTCAAAAGAAAAGTCATACACGAGACGGAAAACCTAAAGGTCAGGTACAGCACAGTATTGGGCCGTATGGTAGCGTGTACTACCCTTCTTGTAACAGCAGTTTTGAAGATATGCCCTGTTTGCAGCCAGGGCATGCCTGTTAGTTGGAAGGACCCTGCATAACCAGCAAGAGGCGTGTGCGCATGCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTATGTGTACTCTTGCACATGTGTAGGCCAAAGGTCAGCCTCGGGTGTCATTCCTCAGGCAGTGACCTTTGAGACAGTTTCTCCCTGATGCAGAACTTGTCAAGCAGGGTAGCTTTCTGGCCAATACATTCCAGCATCACTGGTGTAAATCCCATCTTTTTTGTCACCTCCCCAGTGCCAGGATTTTAAGTACCTAATACCATCCATGCCTGGCATGGTATTTGTTTAACAAATCTTTTTGACTTCATGCTTTCAGGCATGTGTAACACATTTTAAAAATCTCTCCGTTAAAAACTTTGCATTTTCAAATGGATTAAGGGCATGCTTTGTCGTTATGAAAAATTAATACTCTTCCAAATGAAGTGAGGCGGTGAATTGAACCCAAAGGCACACATGTGGCTTGTTGCTAACGTAAAAGCCGTAAAGGGAATACCCTGTTCCCTTTGCATTTTGATACACCACAAAAACAAATAAAAATTACTCTAATGAGTTCCTATCAAAGGCAAGAGCATTATTAGGACTGCCTGGCTTGTGTTATCTTTCGCAATGGCTGACGACGTTAGGAGCTACAAGCATTTTAGTGAAAAGCTGTTTGGAGTCACCGACATACTCACTAGAGATTTCTTTTCCAAACTTGGTTTGAAACGTAGACATTTCTCACGCCCTGTGACCATCTTTTGATGGCCATTGGGAACTGGTGTGATTCTCTACCGAGCAGACGTACTAACAGAGTGAAATCTTTAGTAGAGCCTATTCTCTTTCTAG
Seq C2 exon
ATGGGATAAACAAGTATCCACCGGTCAACTTTAAAGCCAAGTGCAGCAGACTCAGCTCGGCGGCTCCGAAGCTGTCCCCACGCCAGTTTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.062
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=80.8)
A:
NA
C2:
NO
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:
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]