RnoINT0007822 @ rn6
Intron Retention
Gene
ENSRNOG00000019648 | AABR07068316.1
Description
collagen type VI alpha 3 chain [Source:NCBI gene;Acc:367313]
Coordinates
chr9:97956829-97958524:-
Coord C1 exon
chr9:97958379-97958524
Coord A exon
chr9:97956922-97958378
Coord C2 exon
chr9:97956829-97956921
Length
1457 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
ATTTACTTTTTCCTTGGCAGGAT
3' ss Score
9.69
Exon sequences
Seq C1 exon
GTGTCCAAGCCCTGATCCTGGTGGGTCTTGAACGTGTGGCTAACCTGGAGCGGCTGATGCAAGTGGAGTTCGGGCGGGGCTTCATGTACGACAGGCCCCTGAGGCTCAACTTGCTTGACTTGGACTACGAATTGGCGGAGCAGCTT
Seq A exon
GTGAGTCTCTGTCTCTTTTAAAGAGTTACACACACACACACACACACACACACACACACACACACACACACACACACACACACATACACACACACACACGGTTTTAGATTGACGGCATCTCAAGGCAGCAAAGCCAGATGTCTTAGTGGCCTGGTGACTGGGGGAAGGGAACACGGATGGATCACGGACTCCCTCAAGGCTTGCTTTATGGCTGTATGAGTCCTGGATATGGCATCTGTCTTTTCTGTATGATGGAATCAAGAATATGCAGGGAAAGGGACGGAGACCACTTCCAGGTGGAGAAGTCCTCTCCTACCTCCCTTTCTGGGCTCTTCTCTCACTGAGAGCAGCTACCTCCTGGGATGGGGAGTGGGGTGGGGCGTGGTCAGTGATTCTCAGTGACTAAGACTGTGAGAGTCGGAGGGGTGCTGCCCTCTCTTCCTCTGTCTTAAAAACTGGGATGTTTTTATTGAGTGGAAGCAGCTTCAGTCTAGAGCAAGGGGAGCGGCGCACAGGATGAGCACTAATTCAGTGAACGGCAATGTGTTCGGGATGTGTAAGGTCAGGGACGCAGAGGCGGCTGGTGACCCAGATTGTGGAGATCCTGGCTCAGGGCCCAGGGCCCCACATGTTGCCAACCCATTGCTTCTCCAGGGACTCCCCCAGGCCAGTCCTGATTTCCACCATCCCAACCGTGGCTCAGAGAAAGGCGGGAGGTGGATCTCTAATTTAGAATGTTCTTTGACTTCAGGTTGCTTCAATGTGTCGGTTGGGTTTTATGTTTGTGGTTTGGGCTTAAGGAGGTTGTCTTAGGGTTTCATTGCTGTGTGGAGACACCATGACCAAGGCAACTCTTATAACGAAAACGTTTATTTAGGGCTGGCTGACAGGTTCAGAGGTTTAGTCCATTATCATTATGGTAGGAAGCCTGGCACTGCACAGGCAAACATGGTGCTGGAGAAGGAGATGAGAGTTCTATATGTTGATCTGCAGGCAACAAGGAGGAGACTGTGATACACACTGGGCAGAGTCTGAGCATAGAAGACCTCAAAGCCTGCCCCCACAGTGACACACTTCCTTCAGCAAGGCCACGCCTACTCCAACAAGGCCACACCTCCTAATAGTGCCACTCCTTATGGCCCAAGCATCCAAACACATGATTCTATGAGGACCATAGCTATTCAAACCACCATAGAGGTTATACTGAAAATCCAAACCTTGAGTGTCAGAAACTTCTGGAAACTGAACCTAGTCTAGGATAAGAATTATCATAGTTGATTTTTTTTTCTCTTCCACCAACAACTTCCCATCCTATGCAGAGAGCTCAGCCCTCAGCTGCAGCGAGCCTTTGAGGGAGTGGCATTAGGTAGCTTCCTGTAGCAGATTGGGACTGATACCAGCCCCATGGTGTTTTTCTGTTTTCTCTCCTTGATGTGTATTTACTTTTTCCTTGGCAG
Seq C2 exon
GATAATATTGCTGAGAAAGCTTGCTGTGGGGTTCCATGCAAGTGCTCTGGAGAGAGGGGAGACAGAGGGCCCATCGGCAGCATCGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019648:ENSRNOT00000077924:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCCAAGCCCTGATCCTG
R:
TTTGGTCCGATGCTGCCGAT
Band lengths:
238-1695
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]