RnoINT0040231 @ rn6
Intron Retention
Gene
ENSRNOG00000010663 | Col6a5
Description
collagen type VI alpha 5 chain [Source:RGD Symbol;Acc:1565804]
Coordinates
chr8:114583785-114585538:-
Coord C1 exon
chr8:114585485-114585538
Coord A exon
chr8:114583848-114585484
Coord C2 exon
chr8:114583785-114583847
Length
1637 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
TATCCATTTGTCTTTTTCAGGGC
3' ss Score
12.87
Exon sequences
Seq C1 exon
GGATTTTACGGACTTCGTGGGGGAAAAGGACAAAAAGGTGACCCTGGCTCTCAG
Seq A exon
GTAACTTTTCACTAACCAACTAGTCCCTGGTGACAGATCTGGCCTTGTTGGCTGGGCTGGCAGTTGGGGATAAAATTGACAGCAGACTTCCCACCATCTCAGTTACCTTTCTTCTGGCTATGACCAAATGCCTGGTACCATCCAGAAATCCCCAGGAAATGACTAAAGGGAGACAATGCATATTTTGGCTCACCATTCAAAGGTATACAGTCTATTTTGGTGGGGAAAAGCACGGTGGTTAGAAGGTCCTGGTACATGGATCCGACTAGGAAACAGAGAAGAGGAATGACCAATGCTTAGCCCTTTCTTCCTATTCCTATTTTATTTAACCAAGGACACCAGCCCATGGGGAGGTGGTGTCCCCAATCAGGGTGGGTCTTCCCTTCTCAGCTTAAACCTTTTGGGATTGGCTAGAACTCTCAGAGATACACCCAAAGGTATTCCTCACAGTGTCCTGAACAACCGCTTGGGGTCCTTTCTGAACTCAGTCAGCTCAGAGATGTGGATGTCAAGGTAGTTTTCTTGAAACCAGGAATGAACTGCAGTTAGCAAGGCATAGATGTAGAGGAGGAAGAACGTTCTAGACCAAGGGTAAGCAAGCACTTGAGGCTGGGATCCATTGGTAGTTGCTCTGCCTGGAAGGAACAGAGTTCAGGTGGAGGAAGATGAGTTTCAATAGGTTGTAAGGAGAGACTCAGACAGGTCCAGTGAGCCTTGAGGCTGTGTGCACGCGCGTGTATATGTGTGTATGCATACATGCGTGTGTGTTCGTGCACGGAAGGATTTAAACAGGAAGCCATCAAATTTCTGTTTCAGAAATATTTGGAAGTTGTGCAGGGACTGCTGGGGTTGCTATGGATATAAGGAAGGCTTAAGGGTGGGTCTGTAGCGATTGAGGCGAGGTGGGATGAAGCGTTCAAACAAAGCAGTCACAAAAACAGGCACATGATATGCTAAGAGCATGCAGGGACCAGCCAGGGATGAGACAATGGGCACGGTGGTGCAGGAAGCCACTCTCAGGTTATTCAGAGTGAAGCGGCCTTAGTGCTGCTCCCTAGAAACCTCTGTTGGTCCACTGTGACCCTGGCTCAGGGACCAAGGCAGCGGGAAACAGGGAATCAGTCGAAATGCCTTCAGGGACCCTAGTGTGGGTACATTTCCCTGGAAAGTTGTTTGAAGTGACAGCAGAAAACCCCTGGTGAGGTTTCTTGTGGAGAACAGAAGTGCTTGCTAGACAGCCCAACTAGGAGAGCCAGTGTCCATATGTGACTTCCCAAATTTAATAAAAAAATTCCACCTTTCTGTTTCACGAGCCACATTTCAAGGGCTGCATAACCAAAGATGGTGAGGGGAACGTGGAGTTTCCCCACCTGCTGAAAGTTCCATTGGACAACCCTGTGCTAGACCACGAGAAGGTTTCCTGTTTCTCAGCCTGACCATGGCTTAAACTTGAACTTGGGGACTCTAAGGGCACCTGGGGGAGGCAGGAAAGCATGACTTGTTTTATCTGCTTGGCTATCCTCTCCAGTGTACTGCTTGGCATTTAATGCCATTATAAAACCCACCTATAGGATAACACAGATTCATTTTGTTTTGTCCTGTCTGTCTGTCCATCCATATCCATTTGTCTTTTTCAG
Seq C2 exon
GGCCACCCAGGTTCCAGAGGCGCTCCTGGGGAAGATGGCGAGAAGGGCTTCCCAGGGGATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010663:ENSRNOT00000038160:16
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(23.3=100),PF0139113=Collagen=FE(19.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.1=14.3),PF0139113=Collagen=FE(23.3=100)
Main Inclusion Isoform:
NA
Other Inclusion 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]