RnoINT0040263 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114446176-114449956:-
Coord C1 exon
chr8:114449896-114449956
Coord A exon
chr8:114446773-114449895
Coord C2 exon
chr8:114446176-114446772
Length
3123 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
GCCATGTTATGATTTTACAGGCC
3' ss Score
8.17
Exon sequences
Seq C1 exon
ATGCTGCTGATTTTGTTCCTGATGATGATTTGTTTACACGTTTGTGCGAACCAAGATTCTG
Seq A exon
GTAAGAAGAAACGGGAGCACTTCCTTTTCATAATTTTTATTATATGCACTAGCTAGTGAGTATAAGCTGTAAGTTAGGGTGTTTACTTCACCCTGCCTGATTTCAATGCTAGTAAGGTTGTGGGGGCAAAGTTTTATCTCTTTTTGGTTGACCTGCATTCTTTGGAAATTCTGGGCTACTGAGAAAATATAAGAAAGCTATCTTTTTGTCCCTAATTCAGCCTATTTCAGGTTTCCTTGCAGATTCTGTCGGGTTGAGCACTGGAAAGTTCAGAATGTCTCTGTTTTTCATTGACTTGACTAAAAGCATTGCTTTGGCTAATTGTGTGGATTTGCTGCCTGCCACTGCAGGTTGATTGACTCCTGCTTGTAAAAGCAGGCCTGTGTCTACCCCGGAGAGAGCTCCTAACTCTCACTGTCAGTGACTTCGGTCAGTAAATCATGTCCACTGAGATGGAGTTCAAAACACCTTCCCGCACTCCTCAGCCCTGCTTAGCAGTTGGTGTAGGGGCAGCTCATGTCCAGCACTATTTACCCTGCTTTACAGCTTCCTTCAGGATTCTGATCTTGAAACAACTACCACACACCTACCACACCACCTACCACACACCTGACCACACACCTACCACAACCACCCTACCACACACCTACCACACACCACCTACCACACGCACCTACCACAACACCTACCGACACACATCCCCGCCAAACACCCCACACTACACCCACACACGGCTCACCACACCGCACACACCCACACCCACACACACACACACACACACACACACCACACACACCACACCACACACACCACACACACCACACACAGCCACACACACACACACACCACACATCACCACACACACCACACACACCCACACAACACCACACACCCACACACGCACACCAACACACCCACACACACCACCACACAGCCCACTAGCCAACACACACCTACCACACACCATACCACTACACCACCACACACCACCCACCCACACCACACACCACCACACAGCACACCACCCACACCACACACACACACACACCACACACACACCACCAACCGGCGCCGCACACACCACTCCACACCGCACACACACACACACAACCGCACACCACACCTCCTTGCGCGCGCGCACCCACACACATGCACACACACACAACACACACACAACATACACACACACCGCGCACTCTCATGGCTTAGATAGTGATTAGCGACCTGAACTGTTCTCCACTGCTAATCCAGGGCGCATGGTCTTGTCCTACACACAGATAATAGAGTTTATGGCATGTAGGAGAAAGTCACTGGTGGTCCATGTATCAAACTGCCCCTGGGGGCTGGGGATTTAGCTCCGAGCTGGTAGAGCGCTTTACCTAGGAACGCGCAACGGCCTGGGGTTAGGTCCCCCCACGCTTTCCGAAAAGAAAGAACGGGGCGCGCAAAAAAAAAAAAAAAAAAAAAAAAACTGCACTGATCAGAGTTCTTTGGACCAAGCAGGCTTTCCTTAGAAGAAAGTCCTACTGGCCCTCTGCTCCGTCTTCCCCCGAATGTTTCTGGCTCTGTGATCAAGTCAAGAATTTCAGATTACTGGGGAAGAGGTCATTTGAAAGATGAGAAGGGACCAATTTCCCCTTGGAGCTCTGGTCAGATGCTTGCAGAGACTGACTGATGGAAGCCAGGGCTACTTTCTTAGCGATAGCTGAAGAAAACAGGAACTGGTAGGACTTGGTAGGAATTTATCTAGTAACCATTTGCGATAAAAGGCGGAAGTGAGGAGATAGCCTGAGTGTTTGCTCATCAAACCTCCATATTTTAAAGCAGAGGAGACTGGGGCTCATGTATACTGAATAACTTAATAATGATCATAGAGTGAGCCGATGACAGGTAGGTTTCCTGTCACATAATCCAACAGCACTGTATTTTCTCACATAAGGCACACACAAGCACATGCAATTTACCTGTCTTTCTTTGTGACAAAGTGCTGAGAGCTCACAGACCAGACAAAAAGCTGTCAGTAAGTGAAACTAGTTTAGACCATGATTTCCTATAAAGCAAAAATAGAATTGCAGAGCCTAGCATGGTGATGAACCCCGGCCTGTAACCCTAGCACTTGGGAAGTGATGGCAGGAGATCAAGAGTTCAAAGCCAGCCTGGCATACAGGAGACTGTATTCATTCATATATATTTGATTGTATAATGGTAGTATAATATGTATATGTGTGTTGCTCGTGTAGATGCATGTGTACATGCATGTGCATATGCATATGTATGTGTATGTATACTGTCCTAGACGGCTTGCAAATTGTTTAAAGTTCAGAAAGGTTTCTGTGTTCCAACATCAAACATGCTTTAATAGAAACTAAGAGTATAATCCCACTTCTCATCTTAAGTTCTTGGCTGCCATCATATCTTATGTATGAGATGATAAATTTATCAGTCATGATGTTCATTCATATGACTTACTGAATGTATTAGAAATAACTTTTCTGAAGGTGAAGCCAATCCTGTGTATTCATGATGTCTCGAGCTTCATCAGCTCAATGCTTCATAATACAAAAGTAATGTTTTATAAATTAATCAGATAACCTCAGGCATCATTTAAGTGAGACTTGCAGCAAAAGATGCTCAAGTTTCATAGTCCTAACCAGTCTGAAGGAATCTGATTCAAGTGAACATGTTCAATGTCTTGATGTGTAGACATGTGTGTATGTTTGTGTGTGTGTGCCCACATCCCAAACTCTAAAGTACAGGAGGAAATTGCCCATTAAAGAATAAACTACCTTTTTCTTTTCTGTTTTACTTTGATACATTTACCTATTCCCAGTTAGCTAATTGCAAAATGTGTTCATTGTTGCAAAGCTTTCAAATGAAAATGAGAAGCTGTCTAAAGCCCTCACACCAAGAAACAAACATTTCTTTTCCTGAGAGATTATGTGGTGTTAATCTATTCTGTTCAATTTGACAGGAAGGTACTAAAATTGTTTTTCAAAGAAAAAACTTTCTATTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGTTGGCATTAAACGTGACAGAAAATTTCTAAAACTTTTTGCCATGTTATGATTTTACAG
Seq C2 exon
GCCCCGAGTACGCAGATGTGGTTTTTCTGGTGGACAGTTCCGATCACCTAGGGATGAAGTCCTTTCCTCTTGTGAAAACTTTCATCCAAAAGCTAGTCAGCAGCCTCCCCGTAGAGGCCAACAAGTACCGTGTGGCCCTGGCCCAGTACAGTGATGCTCTCCACAATGAGTTCCACCTAGGCGCCTTCAAGAACAGGAACCCCATGCTGAACCACCTCAAGAAGAACTTCGGGTTCATCGGCGGCTCCCTGAAGATTGGGAACGCCCTGCAGGAGGCTCACAGGACCTATTTCTCTGCTCCCACAAACGGAAGAGACAAGAAACAGTTCCCCCCAATCCTGGTGGTGCTGGCTTCAGCGGAGTCCGAGGATGACGTAGAAGAGGCTTCGAAGGCCCTGCGGGAAGATGGGGTGAAAATCATCTCTGTGGGGGTGCAGAAGGCTTCTGAGGAAGACCTGAAGGCCATGGCCACCTCTCAGTTTCATTTCAACCTCAGGACTGCCAGAGACCTCAGCATGTTTGCCCCAAACATGACACAGATCATCAAGGATGTGACTCAGTACAGGGAAGCAATGACTGATGACATTATTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.039
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=WD(100=89.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]