RnoINT0007852 @ rn6
Intron Retention
Gene
ENSRNOG00000019648 | AABR07068316.1
Description
collagen type VI alpha 3 chain [Source:NCBI gene;Acc:367313]
Coordinates
chr9:97966929-97970053:-
Coord C1 exon
chr9:97969451-97970053
Coord A exon
chr9:97967535-97969450
Coord C2 exon
chr9:97966929-97967534
Length
1916 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TGGTCATATCTGCTTTTTAGGTC
3' ss Score
9.24
Exon sequences
Seq C1 exon
GTGAAAAGGATGTGGTGTTTCTGATTGATGGCTCCGAGGGGGTCCGGAGTGGCTTCCCCCTGCTAAAGGAGTTTGTGCAGAGGGTCGTGGAGAGCCTGGATGTGGGTCCCAACCAGGTGCGTGTGGCACTGGTGCAGTACAGTGACCGGACCAGGCCGGAGTTCTATCTGAATTCCCACATGGACCAGCAGGGTGTCATCAGCGCCATCCGCAGACTGACACTGCTGGGCGGCCCAACCCCCAACACAGGGGCGGCACTGGACTTTGTGTTAAGGAATATCCTGACCAGTTCTACTGGGAGCAGGATAGAAGAAGGTGTTCCTCAGCTCCTGATCGTCCTCACGGCGGAGCGGTCAGGGGATGATGTGAGAGGCCCCTCGGTGGTCCTGAAGCAGGGAGGGGCTGTGCCCATTGGTATTGGCATTGGAAATGCTGACATCTCTGAAATGCAGACCATCTCCTTCATCCCCGACTTCGCTGTGGCCATCCCCACCTTCCGGGAGCTTGGGACAATACAGCAGGTTATCTCTGAGAGGGTGATCCAGCTTAATCGTGAACAGCTGAGCAGTTTGACACCTGTTTTGATGCCCTCACCAAGTGCAG
Seq A exon
GTGAGAGGATGGGAGTGGATTTTTTTCGTTTCTCTCCAGATAATTACCTTAGCTACTAGCTTGGGCTGTGAGGTACAAAGCATTTTCAGTCTTGTTTCCTCTGCCATATAGCATGTGTGGAAAAACTAGGAATTTTTTTTTTTTTTGCAAAGCAATAGAGTTAAGATTCATGTCTGTGGTCAACTTGAAGCATCTCAGAGAGCATGCACATGACGTGGATCCAGGCTCTATAGAGAGTCCTGGCGGGGGGGGGGGTGCACACTTGCTGAGTGTCCAACCTAAGTGTCAAGCAGTAACCTGTCATCTGGAGGAGCCTAATCACTAGTGCTCTGCTCTGCCAAGAGGGGTGGAGTCTCTGATATATTTTTATCTGGAGCACCCATGTGTGACACTTGCTTGAAGCTGAGAGGTGTCCCAACTGTGGGAAGGCCTTCCTATTCTCTACATAATAAGCTGACAAAGTCTGAGCTACAATAGCTCAAGAAAGAGACCAAGATGCTCTTCCCCCAGTGCAAGTCAGCCCAGGGCTGTGCCCCCTTCCTGGGCACTCGGGTGGGCTAGTCACAGGGCTGAAGGAGACAGATGCGGGGCAGTGGTTTCATGAGAGGGGGAATGAGGGAGCAGGGAAGGAAGGTGGAGCGATGCATGTGAAAGGAAGTTAGAGGCAGGATTTGTACAGTGGATTTGCACGGCCTGAGGGCTCAGCTTCCCCCTGGTGTTCAGGAGAGAGTGATGTGTTCTTTATATCTATGTGGAATGATTTAAGATGTTCATACTCACATACATTTGGGGGAAGTCTCTGTCTCTGTCTCTGTCTGTCTCTCTGTCTCTGTCTGTCTCTCTGTCTCTGTCTTTCTCTGTCTCTGTCTCTCTCTGGGTCTCTGTTTTTCTCTGTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGACATAGTAGAGGAATGCAGCCATTTCTAAACCCCATTGGACCACAGGAGTATCTATTATGATGCACCTCAAGGCCCTAGGGCTCCTGTATGTGGGGATGGGTGGATGGGTGCATTCCTGTGTGCTCACAGAACCTCCTTTTAGTGAATCCAGACCTATGCTTCTACGGTGCTTGGTTCCGTTCACTCTCCCACACGTCAGAGTGGCCACTGGGTGCACTCCCCACCTTCTTGTGTAGTTCCCTCCAACCCCCCTCTCCCCATGCCTTGCTCTCAGCTGCAGACCAAGTCTCACTTCCTAGAGGATGTTCAGAAGCTCTGCTGGGTCCCTCCTGGTGATGGTTTCATTTCCCAGAGTGATTTTTTTTTCCTGGGATGGCCTGTCTCCACTTCCGCCCTTCTCTTTGAACCTGCTCTGCACACCCTCTTCATGCCTCCTCCACCCTGCTCTAGTCACTCCTGCCCATTCTCCACTCTTCTGGATGATTCTTCTTGTGATAATTGTGCATTGCTCAGACCAGTTCTCTCAGTGGCCTACAGAAGAGCCTGCACCATTAAAAGGCTTACATGTGCTCTGCACGGAGTCTCTCCTGTCTAACTCATTGCTCACCCTTCCTCAGAAAGTGCTTTCTCCAGAGTCCCAGTGGCTGACTCAAAACACTGGTGCCAGGCCAGTGGGCAGTTCCTACCAGCGCTGATGCCTCCTTCCTAAAACAACTCTTCGGTTTTGTCTCCCTCGGGCTCACCTTTCCATGCCTCTTGCTGGTTCCTCTCCTCCTTCGTCTGTCATTCAGATATGGCAACACACAGGACTTGCTCCTTCTCTTGGTGTTTTCCCTATAGTGCCTGATACTAGAGTCTCTCACCCATAGGGCACTGATCTGATGACAGACTGATCCTAGGAAGTGGCTCAAGGGTGATTGGAATATGATGCCCTTGACTGAAGACCATGGTCATATCTGCTTTTTAG
Seq C2 exon
GTCCTGGTAACAAGAAAGACGTGGTCTTTCTCATCGATGGATCCCAAAACGCTGGCGCAGAGTTCCAGCACATCCGTACCCTGATTGAGAGGCTAGTCGAGTACCTGGACATAGGCTTCGACACCACCCGGGTAGCCGTCATCCAGTTCAGTGAGGACACCAAGATGGAGTTTCCTCTGAACGCCCACTTCAGCAAGGACGAAGTACAGAACGCTGTGCGCAGGCTGCGGCCCAAGGGTGGGAGGCAAGTCTACATTGGAAACGCTCTGGAGTATGTGCTGAAGAACATCTTCCAGAGACCGCTTGGGAGCCGGATAGAAGAGGGTGTTCCACAGTTCCTAGTCCTCATTTCGTCTGGGAAGTCTGCTGATGAGGTGGACGACTCAGCTGTGGAACTCAAGCAGTTTGGCGTGGCCCCTCTCACCGTAGCCAGACACACAGACCAGGAAGAGCTGGTGAAGATCTCCCTGAGTCCTGAGTACGTGTTCTCCGTGAGCACCTTCAGGGAGCTGCCCAGACTGGAGCAGAGGCTGCTGACGCCCATCACCACTCTAACCTCACAGCAGATCCAGCAGATCCTGGCCAGTACACGATATCCCCCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019648:ENSRNOT00000077924:5
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:
ACCTGTTTTGATGCCCTCACC
R:
ACACCCTCTTCTATCCGGCTC
Band lengths:
357-2273
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]