RnoINT0040277 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114395734-114400010:-
Coord C1 exon
chr8:114399948-114400010
Coord A exon
chr8:114395797-114399947
Coord C2 exon
chr8:114395734-114395796
Length
4151 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CCTTCCTTGTTTCATTCCAGGGG
3' ss Score
10.54
Exon sequences
Seq C1 exon
GGTCCAAGAGGAGAGGTCGGTGAGAAAGGAGAAAAAGGAGGCTTCGGAATGAAAGGTCCCCAG
Seq A exon
GTAAGTAAGGAGAAAGCAACTGTATCTGGCTTTGACCTTGGCTTGAAAGTAAATGTTTTCATTGTTTCTTCCCTAAAGGTGAATCCTGGTCGCCCCTACCCCGGCACCCCCCCNNGGANNCNGCCNNGGANCNNCNGCCCATCNCCCCCCGGGCCCCAANAACCNCCCCGCCACNCNCGGCAACAAGAAGCACAACGACGGGAGGGCGACGAGGGAAGGGCCACCCGACGGCCAACACAGCACNCGCCAAGAGAAAAGACCACGGAGCGCCAGAGAAACGGAAGCGGAAGAAGAAAGCACGGAAAGGGCCAAAGCACCAGGAAAGGAGAACGAAGCCACAGGCCACAGGACGGGAGGGGAGNCNGGCAAACCCGCACACCGCAAGAGGGGGCGACAAAGGCCACCGGCCCAAGACAACGGACAGGAGGAGGCCCGCAGGAACCGAGGAGGGCCCGGGGACGCCCAGAGACCAAGAGGGGAAAAAAGAAGCGGACAGAGAAAACGATATAGACTGTAGTAGAGCCGGAAGATCCTCTCTAGACTTCCTTGCCTCAGCTTCTCCGCCAACGTTAACCATTCCTTCTCTGTGTTGTGTGGACACAGCACGCCCTGCATGCAAGTCACTCAGAGTTGCCCTCCCTGCCTCCTGGGGGAGCTAGAGCAGTGATTTAGCAGCCAAGGGTGCTTGCTAATTCTTCTAGAGGACTCAAGTTCACAGTCTCCTGAAACTCTAGCATCAGGGTATCCGAAAACCCTCTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTAAGTTTCTTGGGGAGACTGAAACATTTTGCCGCCTGGGACTGTGCTCAAAACTCTTAGAACCTCTGCAGGTGAAGCTTGTATTGTTGATAATAATAAATTGTCCCTAGATAACACCAGGTTTCTCCTTGATCAAAATGTGCTAGGAGTGCGTGAGGATGCAGATCCTGAGCTAGTGGGTCTAGGTCGAGGCTCGAGATGCTGCATGGCCAATGAGTCCCCTCCTGACACTGATGCTGCAAAGCTGGACCCCACATTGAATAGCAAGGCCCTGTGTGATCCGCCCTCCCTGTCTCTAGCTAGCACAGTGTATGTTATCTGTGGGTCTCTTTACATTTTGCAAGCTCTATGCTAGTGTCTTGCTTATGCTGGGTCCACAGTTCCTGGCAACAACAGACCTCAATTCCTTTATGTCATGAATCAAGCAGTAAATGAATGAATGAGCCCCAGTTGGGACTTTCACCCCTCCGCTAACAGCAGTACCGAGGGGAATGCATTACTTTACATGAATTAGCTAAACCCGGGCAGAGGCCCAACATTTAAGTGGTTGCGCTCATCGTGAGAATATTTAAGAGGCCATTTGCATAAACTTGTAAACTGTGGCAAACCGTTTTAGAGTGCATTAATATCTGCTCCTGACAGTGTTTGTTCCTGGCTTTTGATGAAAATACTCTTTTTCAAATGCATGAAAACTTCATAATTTCATGGCAAAACTAAACCAATGATATATATCTTCTGTGTTCACATCTTTGAAGCATTAGAAGCTGGCTGTACCACAAATGGAGATTTTTATTTTAAGAAAGACATGAAGTACAAAGGAAAACATGTATCGGGCTATCTCATCTGTTGATATCAAATATTGATGTGGGGATGTAGATGAGTTGAAATCCAAAGGTCTAAGGCCCCAAGTGGGATCCAAGGCTATTACTCGAGTAATTTTTCCATGTGCCCAGCGGGCACCTTCATCCACTTTAATCTCGCTTTGGCAAGAAGTGGCACAGTCATAAATCATCCAGCCCTTGCCCACGCCAGCTGGTCAAAGGCACCACACCTTCCTACCAGCCCTTCCATTTTCCTCTGGCTGGAAACCCTGCTTTTCTTTCTCTGCCTGCCTTTTATGAAACACCCTTCTTGTCAGATGTTAAAATGGAGTTTCAAAGACAAGTGGAATTTTCTGTGTTTGGGACATGATGAATGGGGTCTCTAGGTGGCTGTTTCTGAAGGAAATCTACAGAGACGAGCGCAGCCTGACGCACAGGAGAGTGCCGTTCTCTGTTGGCCCTACAGACCCTTCGCCATAGGTCTCCTATTGTTTTATGGCACAGGAGGAACCCTCCAGTGGAACGTGTTTTCTTACCTCAGACTTGAAAGCCCTCCTTGGGACTTATGTCTTGGAAAGGGATGAGCTTTGGATTGATGGCCAGAGGCTTATTAACTTACACAGCACTCAGTGTTCTGCATAAATGAAAAGTCCCAATCCAGCCAATATGTGATTATGATTACAAAAAAAAAAAAAAGAAAATGCAAATTGATGTGCTATGCCCTGGAAAACATTTTTGAAAGGAATGACGTCTTCTTTTGTCCCATTTCTTTTGTTGCCCTTAGGACCTTCTCTAAAATCTCCAAATGCAAAGAAACATGACGGGGAACTAGGTCCAAAATACTAATTATACTGGGAGCCGTACTTGTTCTTTGAAATATATGTTCTTAGCTAAATAACACTGGTAGCACGCACACCATCAAGAAAGGTCAGAATTAGCCAAGCATTGGGGTGCTTCTCTACAGGACCAGCACTCAAGAGGCAGAGGGAGGGTGAACCCCCAGACTCTACTAGAGAGTTTCACATTCACAGTCACTCCATTGGCCCTGGTTAAACTCAGTGGGTCATGAGACAAAAAGGGAAGGGGAGAAAGGGCCCTGTAGCGGGGAGGAATTGAGAGGTGAGAGGGAGAAACAAGGGATGGGGATAGAGTAACCGGAATACATTATGCACATGTATGAAATTGTCAAAGGAAAAATATGCAAATAAATACTAATTTTTGAAAAGTAGCAGGGGTAGGGGTGATAATGGGGGGTCCCCATTCTCAGGAGGAGGGGGAAAGGAATGTGGGGAGGATCTGTGTGAGAGGGGGACTGAGAGGAGAAGGAAGCTGATAGTGAGCTGTAAAGTGAATAAATAAATTAACAAAAAGAGAGACGTGGGAGTAGAAGCATTAGGAGTTCAAGGGTCACCTTGAAATTTTGTTTTAAAAAATGTTGACGGGGGGGGGGGGACTGGAGGGGGAGGAGAGTCATGGGAGGAGGGGCTGGAATGGTTCCACAAAAATGGACGTTGCGAAAATTAAATGGTTTGATAGGTGTAAATGCTTGGGACTATGACGGGAACAGTAAGGGCTGTGTAATTATTTTTATTACTATAATATGGTGTCGACTTTGCCTAACAGAACAGCATTGTTTATGCTTTATTAGTGTGAGAGCATACATCCATGTACACACCGCAGTGTGTAAAAGTCAGAGAGCCAGTTAGAACTGGTTTCTCCTCTGCCAGGTACATTTGAGAGACTGAACTTGGGTCCTTGAGCTTGGTGGCAAGCACTATTACCCACTGAGCTACCTCCTGCACTCAAACCAAGGAATCCTGTGTCCTGGAGGTGGTTCGTGTTTTGAAGAGAAAGCTTCCAGGCTTAGAACAATATGCAACCCGAGTTTTAATTGTCTGGCCTCACCATCCACATGATTTAGGCTGGATGGTCTTTGGACTCATCCCTTTTACTAGCTTGACAAGCATTTACAGTAACAGTGGGCCCTGTTCTAGGACACAAAGAGGACCGTTCTCTTTTCTAGCAGTTTATGAAGATAACTTCAGAATCGTTGTCCTGTGCTCCCTAGACACACTTCTGTCACAATGCTAGTTGGTTTTAGTGAAACTTTTTGAGCTTTCTAATGTACATTCTACACTTTGCAAATGAAGATAAACAGCCCTTTGTGCGGGTAGAAAGCATTCTTTGAAGGCCAATGTCCTTTGGAAAGCTGACTTTAAATGCTAGACACTTCAGCAACATCTGTTCCCTGAGCTAAACAGTGGGAACTTAGGCTCATTTGGACACGGAGACTCCTAAAGAAGTGTAATCATTTAGGCCACATCTGGCCAGGGTTACTTTATTAATTTTCTTTTATTTACTAGACTTTATTTGACAGCTACAATATTTTATTTTCCAGAGTAGGATCAGTTCAGCCTTTAACTCTTCCTTCGCCTGTACTTTGTTTTCCGTGGAAGACACGTGAAGGCATTGGGGGAGAGCTGTGCCTCATCCTGCTATATCTGCCTTCCTTGTTTCATTCCAG
Seq C2 exon
GGGCCTCCAGGACCCAAAGGACGAGCTGGGAACCAAGGCCATTGGGGAAGCCAAGGAAGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:22
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(36.4=100),PF0139113=Collagen=PU(13.1=38.1)
A:
NA
C2:
PF0139113=Collagen=PD(3.6=9.5),PF0139113=Collagen=FE(32.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]