RnoINT0040273 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114402560-114409824:-
Coord C1 exon
chr8:114409771-114409824
Coord A exon
chr8:114402596-114409770
Coord C2 exon
chr8:114402560-114402595
Length
7175 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
ATTTTTCTCCCTTTTGTTAGGTA
3' ss Score
9.33
Exon sequences
Seq C1 exon
GGCAGAAGAGGCTGGCCAGGCTCTCCTGGGACACCAGGCTCAAGAAGAAAGATG
Seq A exon
GTAAGAGCCCTTGGAGGCAAGGAGCTTTCAGACTCATGGATCCCATCGCTGTGATGGAAGTCGCTGGTTGTGGGGAGTTGGTGGGATTGTCGATGGCTAAGGATGTTATCTAGAGACACTGAGCTATGTCAGAATAGAACTGGCCTGGTAAGGTCTGGGAAGCCTAAGTAAGAAAGTGCTGGCAGCACACACAGGAAATTACCCACAAGGAAAGACTGCCATGCAGGGAAAGCAGAGTGTCAGTGAGGAGAAAGTGGTCCATGTTTGGCCTACTTGCTGATTTAACTGGAGTTGCCATGATGTTACTTAGTGTACAAGCTTTATTGTCTGCTAAATTTTATGACTATTAAGAAAGTTGGGAAGAAACCCTCCCTTAGCAGTTCTTGATTGACAGTCTAAAGTTCTTTGTCCATATCTGCAGGTCTACCACTAATATCGACATACAGGTCTTATTTAGACAACCATAGTGTTGAGATTTTAAAGGTTATAGCATCCCTGTCATGTCTTAGGGTAGGGGGAGTTGGGGGGAGAATAATGTTAAATATAGTGAACTCATATGTGAAATTCTCAAAAATTAAAAAATGGAATTGAAATAAGTTAAAAGAGAAATAATGGTAGGCATGTAGCCGAGGTTAGACCAGGTAGTTGAATACCTTAGGGATTTTGGTACTGTGATAGAACACAACACCATGACCAAAGGCAACTTGGGGAGGAAAGGGTTTATTTCGACGTACAACTTGCACACCATCACTGAGGCAAATGAAGGAAGGAAGTCAAGGTAGAAACTGAACTGAAGCAGAATCCACGGAGGCATGCTGCTTACTGAATTGCTCCTCTTCACTTGCTCAGCCTGCTTTCTTACACAACTTGAGTATCATGAGTACAGCAATGGTGGTACCACTCACGGTGAGCTGGGCCCTCCTACATCAATCACGAATCAAGACTATTCCCCACAGACTTGCCTGCAGGCCAATGTTATAGAGGCATTTTCCTCTATTAAAACATCCTCTTCCCAGATTTGTGTCAAGCTGACAAAAGCTAGCCAGCACATTGTGGAACCCATTGGGGGAGTTTTATTTTGTTCTTAGTTTATTTTATTGGCTTTGTTTAAATACACGCTTTAAAAATATTCCATGTGTGATTGCTTAGAAAACCACACAGATTCCAAATAGAAAGCCTTTATCCAATAAGAGATTATTTAAAGGAATTCACTTCCACACCTGCATTAGAGTCTAAATTATACCAATTTTGTCTCATTTCACAGCATTTTCTTTTCCAGTCTTTCTTATCCAGCCTGCTCACCCCGTTCCTCAAAATGCAAAATGTCTTAAAATTGAGCACAAATAAAAACTAGTTGAGTGGGTGGCAGTCAGGAGGCATTGTGTTTTCTGGGCAGAAGTAGTTAATGAAACTAGCTATTACACTCCACCAGGAAAGTGTTTTTGCATCTGGAAGCATACCCATGTTCTTCAGGCGGCTGGGAAATAAGAAAATAGGAGCTGCGATTGCATTCAAACTGTGCAGAGTGTGATTGTTAGCAACCAGCTTTGCTAATGTTGCTTCAGTGCATATGCAGATGAGGGAGTGTTTATCCTCTGCTCTTAGTTTTCTGCAATGGCATCTCTGTGGGCTTACATCCCCCTGCAAAACATTGTCAGTGTTAAGAATATCAACCTAGGAAGTCGTGGTGTGAAGAAATGTGTATTTTTTGTTTTGTGCCCCCCCCCAGAGGTCATATCAAACCACACAGCTTCCAAGGAGGAGGTCCCCATGTTGGTGATAGGTGCCTCTGTGTCACGCAGGAGTCAAAGCAGGACTCCTGCAAAGGACAAAGCAGGGGCACACCTCGGCTATAGTCCTCTTCTGTGCAAGTCAGAAAAATAAAGTGAAAAGACTCAATGACCCCACCTTCCGGTCACAGACAAGGACTGACACCAGACAACTAACTCTGCATGTGGACCACAGAGAGGAAGTTCACTGCTTAGCTCTGACGCCAGGACTAGATTTCTCTCAGAGTAACTTTACCATCCATAAGGAACTGATCAAGACAGCTCTTCGGATTTGAAATGTCGATTCTGAGAGGGACAGGGGATAGCCCCATATATCCCAGTGAGCAGAGGAGGGTAGCCCCATATATCCCAGTGAGCAGGGGATAGTAGCCCCATACATTCCTGTAAGCAGAAGAGGCAGAAAAGGATGGAGAGACACTGAATTGTGTTTTGTTTGGATCACTGGTGGCCAGAAATCTAGGCCAGGAAGGCTGCAAACAGTCAGGGACAGCGAGTCTGTGAAGATTGAGACAGATACTCTGGGACCTGGAGGGCTTCGTAGGAATCCCAAGAATCTCCTAAATGCCAGAAGTTGGAGGAAGATGCAAGACTTCTCTTGACCCCAAGGTGTTTTAGAGAGTGTCTCTATGTCCCACCAGACCTCCCCAGGGTTTTTAGTCTACAGGGTCCCTTCCAAAGATGGCCAGTCTTTGTTGCCAATGAGTCAGAAGATTAACTAATCAAAGCACAAAAGAGAGTGGGGATAATCACATCCAAATGGCAAATTAACACCCACCCCCCTGTCCACCCTTTCCCCATCAGAAGAAGAGTTACTGGAAGGAAAGAGAAACTCTGGCAAACAGATCAAGTCTGAAAGAACTGAAGCCTACATTTTTGCTGAGTGAAAGCTTCAAGAATTGACAGGATGAAAGTGAAAAGAACCAACTGGTAGACCTTGAGCACAGGAAGGCAAAAAGGAAGTGCGATTTGGCAGGGCAGCAGAAATGGCACCACTGGGCTCTGGGTTCCTTATTTTTACTTTTCTATTCAAGAAAAGCTAAATGTAATACTTATATTTTTAAGATTTTATTAGTTTTTTTATGCATATGAGTATTGTATATGTCAGTGCACCCTTTCATGCAGTGCCCATGGAGGTCAGCAGAGGGCTTTGGATCCCCTAGAACTAGAGGTACAAATGGTTGTAAGGTCCCGTGTGAGTTCTGGGAACTGAACCTGGGTCTTCTGGAAGAGCAACAAGTACTGATCCAACTCTCCAGTCCAATACTGAACTAAAATAATCACGTGATTTGATAAAAGTGCCATTGTGTAGAATGCTGCCAGAAAAATCCTGTAAGTGCAGGAATCATGACTATCAAAAGCCAACGACTACTTCTCTTTTCTAGATCCTTTTCAAATGAGGACACCTATGCCTGGTGTCCTCAGAGGTGACAAGAGGGATCAGATTGGTTCCCCTGTGTCTACAGATGGTTATGAGGTACCATGTGGATGCTGGGAACTGAACCTGGGTCCTCTGAATGAGCAGCAAGTGCTCTTAACCTGAGTCATCTCTCCCATCCCGCTAATGTTTTTTTCTTTATGGAGGATTTGGGATGATTTTGCATTTTTGCTTGACCTGCATTCAAATATTAAGTAAGGATTTATTATTTTAATAATTGCAAGAAGTTACTCTTTAAGAAAAGATGTTATGTATAAAACTGTAAAGTACAGGTAGATGGTGGGCTGAAGGTGTAGCTAAGTGGCCGAGTCCTTGTCTCATGGCCGAAGCTCTCTGTTCCATTACCAGCACTTTATATAGCCACAAAATATGGATCTGGATGAAGGACATTGAGGAATCCTCAGTGCAATAAAATGCTGCTGTTTTGACAAGTGGGTAGAGAGTGGCCAGTAGTGGGGACGGAGCATGGCATGCAGGGAAATGGATATCAACAACCCAATCTGATCTCTCTTCACTGAACAAACACTGAACACCATCAATGAGCCAGCAACTCGCTGAGCACTAGAGCTAAGAACTCAAACAAGAGTTCTTTTCTCTGCAGGAATTAAGAACCCTGGAGTAACCGTGGCAAAGTTTCTCCGCTTTGTTTGAAGCATTGCTTGTAGGGAATGGCTGCATCCTGCACAGAAAGAAGCTCATGCCTTCCCTGACCTGAGCTCATGGGGTGCCAACAGCACACCCAACAAGAAACGTCCCCAGACTTTGCTAAATGCTTCTTGGAGAGGAAAAAGAGGTGGCAAATCCCTCTTCTATTCAAAGGTAACTGAGGGAAAGAGAGGCAGGCCTGCCCAGGGAACGAGTTATTATCAGAGTGAGGCCAAAGTACAAGCCTGGACCAAGGGCAGGAGAAGCAGCCAGGAAGTACAGCCTGGGGCATTGGCGGGAAATAGGAAGGGGTGGCGCCCTCTGAACCAGACTGTGCTGAGAATTGGAACAGATCCTCTGCCAGGGGTAATGAGAAGCAACTGTAGCCTCAAACGAAAGCAGGCTTTCATTCCAGTTTGGCCCAGATTGTTTTTATGGTATTGTCCATTCATCCTTCTGGGTACCACTTTACAGGCCTCCCAGAAAACGCCAGAGCAGCAACACTGGGCATGAGCCTGCCAGTTAGATTCAGGATTCATGGTGTATCTGCCATTAATACCCTGCTTACTTCCTGGTGACTGTCTGTCCCAAATTAGTCATATCTACCCATTAAACAAGGTTCTCTTGAGTACCCAGAAAGCCAGGCTGCGAGAACTATGGAACTGGTGACTCTGTCTTACATCAGGTTTTTTCTCAGGTCCCCTGAGAGTACTTTCCTTCCTTGATGTGCCTGCTCACATTTGCTTTAAAGAGGAGTCAGGATCTCTGGGGGTGTGAGCAGACCCCAGTCAGCCTTTGAGCGTACCCTTCTAGTAGCCTGAGATTATCTTTCCTATGTAAACCCCTTGAAAAGGTTAGGCAAAAGCTGAAAATTTGCTTGCCCTAGTTCCTTGTCTGCTTTCCGTGTCTCATGTCTGCCAAGGTCTCTCTCCCATGACTTTGTAGTTTAAAGCAGCACAAGCCCTGGGTGGCCACTCCTGGGTTTGTTCCTGTCACTTATGTAATCTTAGATGTCAAGTTTGGTTTCTCCCATTAGGCCTGAACCCCCTTGACTAGGGACAAGAGTCGGTTTTTGCTCACCACACCAGCTCCCCAAGCCTTGGACAGAACAGGGACACCAGAGATATGATGACTCCTGCCATTGAGCTCTTTCAAGATCCGATCTTAAAGTCATGTGGGAACATGGCGGGAGAGATTGCACAGGTGGTGTGCTTGCGGGAAAGCCTGAGGTACTAAGGCTTTACTAAGGCCACAGAACATAGCTGGATGTGGTGCTGTACTCTTTTGCTCCCAGCATGGAGAGGGCAAGCTAACAGATGCCTGGTACTTGTGGGTCAGCTATCCAGCCCAGCTTCATTGGTGAGCTTCAGGCCAACAGAGAGACCCATGTCTCAAAACATAAGGTAAATGGCACCTAAGGGATAACGCTGGAGGTTGTCCTCAGGCATACACACACAAGAACATAACAAAAGACAAACAGGAGCAAATGTCGATGTTTTGAACTCTGGTTCGAGAGAAATATCCTTCATGTGAAGCTCTGCTCTGCAGTCCTTAAAATTTACTGGTGAATTTTTTTGTTTTACTAGAATATAACATTCTTCTCATCTCCACTCCAACCAGCTGTATTCACCGGAAACATGGTCCAACCATGAGTGTTAACTGTACCACAGACCCCAGAGGCTACTGCTGAGTGTGGGACAGGCCAGTCAGCCTAGTGCCCCCACAGCTCCCATCTCCTCTCTTATCCCTGTCGCCAGTGTCTACCATAACTCCTAGTTTCCTGCCTCCATTACCCAGACTAGGTCCCTGATGGAAAGATTCATACATATCCCTGACACCAAATCTCTGGGAAGATTTCACATCTGACCAACTGGATGTGATCTCTGTCTTTGAAACCTCCTTCCTGTCCTTGGGCATGTACTGTGTCTGCCTTGTAAATGTTTATAATGTTTATCCCTCCTCCCCCAATACTTGGAGAGTGTGGATATTCCAAGTTCAAAGACTCAGGGCGGGTATGTGTGTGCTGGAAGGGGGTGGTTCCTATCTATTATCCTCTAAAGTGAAGCAGATGGTTTTCTGAATGAAACTGATCTACTGGTGGATATTTTTCTGAATGACGTGGATTGACTTGAATTGGAACAATTCATTGTGCAAAACAGAACAGATTATTATTTAACTTATAAAAATTGCATGCATACGTGTGAGTGTGTGAACATATGTGTACCACACGTATGAAAGCCAGAAAAAGATGTTTGAGCCCTTAGAACTGGAGTTGTAGGCAGTCGTGAGCTGCCCGATGTGGGGTCTGGGAACTGAATCCAGGTCCTCTGCAAGAACAGCAAATGCTCTCGGACTCTGTCTGAGCCATCCTTCTAGCCTTTTGAAAATGACTTCCTTTTCTTCTCTGGCAGAATTTGGGCCTTGAAGATGACTTATTGTTTGAAAGAAATGAGACATCCCCCGCCCCACACACACACACCTTTGATTCTTAGATGACAACATATTTTGTAATACACTTAGCAATACTGGCCTGTCCAAACATTTTTCATGAGTTTGCAGCAAGCCAGTATTGTCTCATGGCTGTTGGATTTTCTGAACTCTGGATGCGAGTTTTGTTCTGACTTTATTAAGTGACCAAGTCAGATAGAGCATGTCATTGCCTCTTGATTATCTGAATGACAGACTACTGATTGGGAAGGTACCTCAGACCCTGACCCTTTCCTATTTAGCAATGTTATGGATTGGGTATATTATTGATACAATGGATCAAGTCACTTTTGAATACTTGAGATGACTGGTCTCCGACAGCTAATCACATTGCTTGGCTTTAAAAATCAAACTAGTTTTGCTCTTTAACTTCTGAACTCAGAAGATTTATTATGAAGTTCCTGGAGTTGATCCTCAGTTTTTCCTCTGGCATCCTGCCCCTTGGCTGGTCCATCCCTGATTCCTGACTGACTTTGTAGTGCTTGGGGGAAAATAAGGAAAGTAAGATCAGATCAGTCAGTGTTGCAGCCGAGGAGCAGGTCTGGTCGAGTCTTGTGAAGGTGTGGGCCGTTAGCTATGACCTGTTGGCTTCAGGTTGTCTGTGGTTTCAATTACCTGTTCCTTGCATGGGAGTTCAGAGTCGTCCTATTCTCACAATTCACTGAGGAATTGAATGTGTTAAGCACAATGTGGGAGTTATTTATGTCAGTGCCTTGAGGTATCTGTTACCAATTTAAATCATATACATGCACATATATATGCACACACATACCCAACTTTGTTAAACTAAGTAGTACTATTTTTCTCCCTTTTGTTAG
Seq C2 exon
GTAGTCATGGCCGAAGAGGGACATACAAGCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:19
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=PU(13.6=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
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]