RnoINT0040287 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114366456-114373327:-
Coord C1 exon
chr8:114372834-114373327
Coord A exon
chr8:114366553-114372833
Coord C2 exon
chr8:114366456-114366552
Length
6281 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGC
5' ss Score
9.86
3' ss Seq
CTTGCTTCTGCTTCTTCCAGATT
3' ss Score
9.94
Exon sequences
Seq C1 exon
GAAAACCTGAGTGCCCAGTGCATCCAACTGAGTTGGTGTTTGTCCTGGACCAGTCCCGGGATGTCACAGAACAGGACTTTGAGCGGATGAAGGGGATGATGGCCTCCTTAGTTAGGGACATCAAAGTTAGGGATGCCAGCTGCCCCGTGGGTGCCCGCGTTGCCATCCTAGCCTACAACTCCCACACCAGGCACCTCATCCGCTTCTCGGATGCCTACAGGAAGGACCAGCTGCTCAGGGAAATTAAAGCTCTTCCTTACGAGAAATCCTCCGACAGCAGGGAGATTGGCAAAGCCATGAGGTTTATCTCCAGGAATGTCTTCAAGAGAACCCTCCCAGGGGCTCACGTGAGAAGAATCGCCACGTTCTTTAGCAGTGGCCAGTCAGCCGATGTCCAGTCCATTACCACAGCTGCCATGGAGTTCAGTGCCCTGGACATCATACCAGTGGTGATTGCATTCAGCAACGTGCCCTCGGTCAAGCGTGCCTTTTCG
Seq A exon
GTAAGCATTGCCTAAAACACCTTTTGTTCACGTCCGTCACCAATATTCAGAAAGCCCGTAAGAAAATATATAGCTACATTTTCTTGCCTTCAGCACAAGGTCATTCCAGGTAGCGAAATACAATGCTTCATTGCTACTTATCAAGCACTGGATAAGCTATGTGATCATTTTCCTTTTGAATTCTCGCAACTACTGTGCAAAGATGGAGATGGGTTTTTCTCATTTCATAGATGAAAAGGCTGAGCCCAGACAAGGCCAGCCGCCGGTCCAGGTTCCGCAGCTGCCCCAGCAGAGTGGCGATGTTAGGGTTTGATACTCAGTTTGCTTTGCCATGGCTTCCCTGGCTCTTACTGTGTGACCTCTGCCTCCAAAGATGCTAAAATCAGGAGCTCAGTAAACAGATATGAGTGTCCGCGAGATGATCATGATAGTGGTCATTGCTGGGTGGTTTTCAAAAGTTAGCTAATTAGGTGTGGGGGCACACCCCTGTAACCCCAACACTTGGAAGGCAGAAGTCTGAGAACCAGGAGTTTGGGGGCATCCTTACCTACCTGGTGAGTTCAAGGCTGGCTTGGGGCCATGTGAAAATCTGTCTCAAAACGTAAGCTGTGGCTCTGTGGAAGTAAAGTGCATCAGGTCCCCAGCACCCATACGAAGGCTAAGCATGAATATAAACCCAGCGAGGGGCAGTGACAGATGGTTCCCTAGAACTTACTGGCCAGCCAGCCCGAAGGAACTCTAGGTTCAGCTGCCTCTGTCTCAAAAATTAATGTAGAGAGTGACTGAGAAAAGACATCTGGACAACAACATTTGGCTTCCCCATGCATGTCACATGCATGTACAAATGCACAAAAGAACACATCCATGTATCACAGCTACATAGAAGCAAAGTAAATAAACAAATAGGCTGATTTAAAAAAAAAAAACAACAACTCCAGTTACGTAAAGGTCCCCACTTTATAAAAGAAAAGCCATTCCAACTAAATGTCCTTAGATTAAGGATCAAACCTAACATGTAGCATCCCTCAGTGAACCACCAGGGATGGAGACATCCTCGTACAGTGTAGAGTTTCACAACTCTCCATCCTTCATTGCAAAGACTCACTGGCCCCAGCAAGGCATCCTTCCAGTAGGTGCTGCTCCAGCATGATGTTGGGTTCCCCGTTCGTGGAGAGCTCCGGTCAGCAGTACGAGAGCGTTGGGAAATAAGTCTGGCAGTTCATGTAAAGAGTAAGTGGTGTGATGCTGTGCCTCGGGACCCAGACCGTTCTAGCAAGCACAAGGATGATTAGCTTGGCTTTTTTCAATAGCTTGATGTTGTTTAATACTAATGGGTCCAGGGTGGCACAGGAGATGGAATGGCTGTTAGCATCAGTGGACTCAGAATTATGTTAACAAGAAAAAAAAGGCTGATTCATCCAAAGGATACTGTAGGTAGATTAGGAAAGGCTGTGGCTGGGCCATGCAGACGGAGCCTGGAATTCCTGCAAGTGATTTTGGTGAGAGAGTCCTTGCAAGTTTAGTCATAAACAAAGGATAATTTCTTATCCTGATGATATGAACACTTGGTGGTATTTGTGACAGGCACTTTAAACTGACAGTTCTCCATCCACTCAGAAAGTACACAAAGAGAACACAGTGTACAAAAGGTATTGTGGTTTGGAGTTTAGGTGTTTTGGTTTGAAATTTATCAACTTTTCAGTGTTAACATCCACGAAGACGGGTGAATCTAGTTTCTTGATTCTACTTAAATTGTCTTTTTAAGTAAAGCTCAATTTTAAAAAGTTGAGCCCCGTGGGGTAGGGAGACGGCCCAGTAGTGAAGCACTTTGCCTGAGGTCTAGAGTTAGAGTCTCCAGAATCCATGTAAGCTCAGTGAAGTCATGAGTCTGCAATCCCAGAACTTCTACACAGGGATGGCTGCAGAGAGAGAATCCCCAGAAGCTCGTGGGCCACAGCACTGAAGCACACAGCAGTTAACACCCCTGCCTCACACACTGTGGAAGACAACACCCAGTGCTGCCCTCTGACATGTTGAGAATATGCAAAGCTGCTGCTGCTTCCTCCTCCTCTTCCCCCTCCTCTTCCCCCTCCTCTTCCTCCTCCTCCTCTTTCTCCTCCTTCTCTTTCTCCTCCTCCTTCTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGTGTTGAGACAGGGTTTCTCTGTGCCACCCTGACTATCCTGGATCACAGAGATCAGCCTGCTTCTACCATCAGAAGGCTGGGGCTAAAGGCATGCACTACCAAGCCCAGTCCCACACATTTTTATTATTAATTTAAAAACAGCCACAAACCTTATAAATCTGGGGAGCAGCAAGTGAAGGATCTGAGGTCAGAATGGGTCCTAGGTTCATTATGGTATCACATGTTGGGCTCTGAAGCTATAAGGAAGAGCTGGAGGTCCCTAAGCCCACTCTGCCCTTGAGGGGCCTAGGCTTGCTATCTAGGGGAGCTTTAAACAGAGGCAAGCATGCCAACTGGTTAGAACCAGATTCCAGATGTAGTGAGTGGAAAGTCACTTTGCTCTATTTCTGCCTTTTTGGTTCTGTGATCATTTTCATTCCCCGTGCCTTCCCTGGACTTAAACTCTTAGTTGTTAATCATTATTATTCTGTGGTTGTTTTGGTTTGGGGGAGGGGGATTGGGAGGTCGTTTTGTTTTGGGGATTATGTATCCCCAGCTGGCCTAGAACTCTCAGAGATCTGCCTGGGGANNACCCTGCCTCCTGAGTACCTGGACATTATTAAAATTTTCCTTTAAGAACAGAACCCCAAACTCAAGTAACATGAGGGTCATATTTTAAAATGCCCTTCTCACTTATCACAGTTTGTCTAAATCTCAGTTCAGCTGAGAGCTGAAAAGGCCTGGCTGAAATCTAGTAACTGTGCAGTTAGCCATGTGTCAGCTCTAAAGCCCAGATCACCCTTGGGTGCTGTGACAAAACACCGTGGCCAAAAGCAACTTGCAAGGAACACATTTATCCTGTTTTCAGTTTCACATCCTAATCCATCACGGAAGAAAGTCAGGGCAGAAACTCACGCCAGCAGGAACCTGGAGGCAGGAACTGATGCAGAGGCCATGGAGGAGGCTGCTTACTGGCTTGTTCCCTTTGGGTTGCTCAGTCTGCCTTCGTATAGCACCCAGAACTACCTGTCCAGGGACAGCACCACAGCCTGTGGGATGGGCCCTCTCACACCAGCCAGCCCTCAAGACGGACACACACAAACGTACCTATAGGCCAATCTTACAGGAGCATTTTCTCAACTGTGGTCCCATGTGGGTCTCATAGAACTCTAGCTTGTGTCAAGTTGACGTAAGTCTCGCTAGCACAATTGCCCTCCCACAACCCTCTCTGTGCATTCATAAGAATAAAAACCTTCCAGCATATTAGAACGCCATTTTTCTTCTTCTGTGCCATATATTATGTAGCCCTGTGATGTCTATGAGAGAAAAACCATCCAACCATCTACAGATGGCCACACTTCACCTACAGCCTTGTTAACTATACTCTCAGACATGCTGGTGCACCTTTGCATTTTTTTCTTTCAGGAAAATAAGCAGTGAGAGAAACACAGAAACTTACCATTGTAAATCCTCAGCTCACATTCAGTCTAGAGATTTTTTTTTTTATATAGATACTCCAGTAACTCCATGCTAAGCAATGGGATCAGTGATCCCTAAAACCACCTCTTTCAAACCGTATGAAGAGATTACTTGCTGGGGCGTCGGGGAAATGCAGGTCGCCAGTGGACTCTTCCTAACAGAGCAACTCATTAGAATGTGTGAGGAAGATCTGTTTCCCGTTTTATAACCTTGTGCGGAAAAATCATTAAATGTGAACATCCATTATTACACGTGGTCGTTGCCAGAAATGTGGAAGTTGTTATGCTGTAGACACATAGAACACAAAGCTAGTTAGCAGATGACAACATTCCCTGGACAACCTCCCCAGAAACATCACTCTTAATTAAGTAAGGACCCAGCGATGCACAGCCAGACCATAAAAGCGACTGGAGCATGGAAACCCATTCTTGTGAGAGATGAGCAAACCTGGCCCTGAAGCCTTCTGGACCCCACTCCTATCCCGGGCTCACTTTTCCTTGCCTGGAAAGCAATGAGGCTGGCTTATTTGGTTTCTAAATTTCCTTCAGGCTTATTCTGTACCATGGCTGGCAGCAAGAAAAATCCTTGCGGCCCTCTCCCCCGCTGTCTGTCCCACACTCTCAGAGCTGACTGACTTGGTTGCTAGTCACTCTTCACAGGAAACCATTTGCACAATCTATGAATGAATCAGATGCTGCTCAAGATGGCGAGAGAAAGCAGAGCATTGCGTCCCACTGCACGAAGTCCCCATCTGTGTCGCTACAGCGCCTGTGCCCCTCACCACCCAACCTCCATGTCCGTCCCCTTATGACACATCATGCTTGCTTTTATTGCCTTTTGCTTCCTCGCCTTTCTCTGGAGTGCTCTGCTCCTTGCTCTGTGGATCTGAGTCTATAACCTAAATCTTCAGTTTTCACAAGAGCTTCAAGCCTTTACCTCTAACCCAGGCGGAATAGCCAGGCAAAGAAAGCAGTGGGCAGCTGGAGAGGAAGCTAATGAGCACAGACTTGTCCATCTGCTCTGTGCAAGATAAAAAACGGGCAGAGATAGGGCCAAGTCTTAGGGAGACACCCTCCTCCTTCCTTCCATTCCCCTCCTTCCTTGGTCTGCCAGATAGAGCATAGCCCACTGTGTAACTGCAGATGGTTACTTCAAGACCACTGGATCTCATCCTGTGCATCAACCTTTGGTGGTTGAATGACTCTTTCACAGGGGTCGTCTAAGACTATTGTTAAATGAGTATTTACAGTGTGATTCATAATGGTAGCAAAATTACAGCTATGAAGTAGCAACAAAGGTAATTTATGGTTGAGGGTCAACCCAACATGAGGAGCTGGACTGAAAAAGTTGAAGCACTAGGAAGGTTGAGAACCACTGTTCTAGACAGTCTTGCAGCCCTTGGGGCTCTGATTCTCAATTCCTAAAAGGACAGTTCAGATGCCCTGCCAGGGTCCAGTTGGTTCTAGTCAGAGAAATGATGTAACCCGACGTAACCAGGACGTCTGTGGTTGCACCTCTATGGATTAAGTGTGGGACTCAGACTCGTCAGGGAGAGAGGAGAGCTACTTTCTTGAGAGTCTAAGAATGATTCAGTGGGAAACAAACATCGTCTGACCGTCACATCTTAGCCACAGGATAGGATCACTGTAATTTTTCTTCACCTATTAGTCATCTCACAGTTGACGGGCAAGTTTGCTAATCTTGGTCACTTGGGGCGTCCTTATCTACTCTTCTTGCTCCCTGAGCTGACCCTGGCTTAGTCACCAGTCACTCATCGGTGTTCAGGTGGGCCAAAGATGTGGTTTGCTTGAAACACTGTGGATGCTCTAAAAACCACTGACAGTGCAAAGTCACTTCTGCTAGCGCACAGTCAAGCCTGCATCCTCTAGCTCCCTAGACGGGCTACTGATGGTGCTGCTGCCATGGCGGGACCCGGATGTTTCAGGGAGGAAAGCCACTTAGGCCTGGGCCTGAGACGGCTTCTGTCACACCTAGTTCATGAGAGAATGATAAAGCAGTGTCCTGGCTAATTTTGGTTGTCAACCTGAAGTGTAAAGCGTGGCCCTTGGTTTCCTAGTCCCCTGGGGACTTGGTGTGAGGTGCAGGGGTAGGGATAGGGGGCTGGGGACTGGGGTAGGGGTAGAGGGGATGGGGGGACGCAGGGTCTCATTCTTTTCCATAACTGACTTGAGTGTAGGCAGTCTCTCTTGACCGGTGTTCTTTGGTTCCTCTATATGAAGAAGAATAAGGACGGGGAATTCCCCTGTTTGGCGGAGTGATATAGTTAGGAAACGTTTTATGCTCTCTGCTGACCCATGTCACCCACCGTGTGCCACTGACCTATCCACGTCACCCACTGACAGCTTCACGGTGGTGATCTCTGGACATTCTATTAGACACAGTAATAGAATTCCCCTTTGACAGCTAAAGGAAGAATGGAGGGTTAAAACCAGCCGGGCCACCTCCCAGCAGCCTTGTGGGTTTGCCCTCCTATGACCTCAGCTCTCGAACTAGGCTGGAAGGTTCCAACATCCCAACCCGCTAAGCAGTTCTCTCTCTTGCTTCTGCTTCTTCCAG
Seq C2 exon
ATTGATGACACTGGTACATTCCAAGTCCTTGTGGTTCCCTCCAGGCCTGACCAAGTGCCAGCGTTAGAGAGACTCCAGCGGTGCACTTTCTGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.091 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(92.8=93.3)
A:
NA
C2:
PF0009223=VWA=PD(6.0=30.3)
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:
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]