RnoINT0040210 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114697601-114699208:-
Coord C1 exon
chr8:114699146-114699208
Coord A exon
chr8:114697637-114699145
Coord C2 exon
chr8:114697601-114697636
Length
1509 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
TATGTTTCTATTCTATCCAGGGC
3' ss Score
8.59
Exon sequences
Seq C1 exon
GGCAGTTCTGGATTTCCTGGGTTTGCTGGAACTCCAGGTGACCAAGGCCCACCAGGAAAAATG
Seq A exon
GTAATGGGAACCTTTTCCTTTCTTGTTTCCAACCTTGTGCCAAGATGAGTAAGAACTTGATAAGAAGCCTCACTGAAGAAGAAACAAACATCTGGGACATTCAGCAGGTTCAAGGGACCTGGCAAACAGCTTAGCAAACTAATGTCAAACCTACACAGTATTCTAGGTGTCGTTTTTCTCTGAATCCAGAGGTGATCTTGGAGTGACTAGAGGTTTATGGGTCTTCCTGAACGCATAGATTAATACATAAAACTTACCAGAGAATGAGCTTATCAATGCAAACACGATGACCAACACGTAAAGCCGGATGGAAATCCTCATTGAATATTCCATCCATGCTATCTTAACTGAGCTGATGCTGCTACAAGACAGAGGGCTTTTTCGAATACAATGAGACATAGAAAGTCTCGGAAGCTTTGCCCTATGCTCTGCTTTAGAGACAGGGTGGGATAGTTTGCTTCCCTGTGAGAAACCACATCCCCCCACTGCAAGTTGGGGAGGGATTGGTTTATTTGGATTATAGGTTACAATCTGTCATTGAGGGGAGTCAGAGGAGGGACTCAAGACAAGAAGGAACTTGATGGCCAGGACTGAGGCAGAGACCATAGAGGGATGCTGCTTACTGGCTTGCTCCCCTCACCTGGGATGGTAACATTCTAGACCCATCTGTTTAAGGGTGATACTACCCACACTTGGCTGGGACCTCCTTTGTCTGTTGGCAATGAAGAAAATGCCTCACTGACACGTTCATAGGCCAAGCTGAGGTGATTCCTCAATTGAGATTCATCCTTCTGAGATATGCAAAGGGTTTGCATTAAGTTGATAAAAACTAACCAGTGTGTGTCTGTCATTCTGTGAGGCATAACGTATTCATCAGCCAGAAGGGGACATCAGAATATCCCTCACTGGAGTTCAGGGTTTTTACTGGAGAGAATCAACTAAGTAAAAAAAAAAAAAAAACCAATCAGACATCACAGAGGTAGTTCATGGTCATCTGGTGAGGGAGCACAGACTCAGTGGGTTTCAGGACAGTGACCTGCCCAAGGCTACAAGTCACCACCCTGTAGAGTTTAAACAAAGACAGTAACTGTCGAGGCTCCCAGAGGGGCTGGAGCCAGACAGTGGTAATCGGAAGACTTCTGGGAGGTTCCTTCACTATGAGGGCAGAGATGGGGTGGGGATGAGAGGCCTGGAAGAGCAGGAACAGGGGAGATACTGGGACGTACTTTAGAATAGCTTCTGCTAGGACCTGGGCTCTTGAATGGTTTCAAAATTACCTGGTCTTCCAAGAGTCTATGTCCCATCCTCCTGGACTCCCTGGACTCTGAGGTTTGGGCTGTTCCAGTCAGTTACTTTGTCCTCCTTACTGGGCTGAGCAGAACTCAGGGACCAGGAGAGGAGGGCAGCGTATGTGCCATGGTGAGCACTTAGCATCTCCAGTTGCTTATAGAGAAAAAAGTGTTGGGAACCAGAATTCTGCAGTTCTAACTATGTTTCTATTCTATCCAG
Seq C2 exon
GGCATCAAGGGCCCAAAAGGCTTGGCAGATAGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:28
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=0.667
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.5=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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]