RnoINT0039789 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83389400-83390695:-
Coord C1 exon
chr16:83390504-83390695
Coord A exon
chr16:83389687-83390503
Coord C2 exon
chr16:83389400-83389686
Length
817 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CTTGTGTGTTCTTCACACAGGGC
3' ss Score
9.74
Exon sequences
Seq C1 exon
GGGAGCCAGGCCGTCCAGGGAGCCCAGGCCTGCCAGGGATGCCAGGCCGCAGCGTAAGCATTGGCTACCTCCTGGTGAAGCACAGCCAGACGGACCAGGAACCCATGTGCCCCGTGGGCATGAACAAGCTCTGGAGTGGGTACAGCCTGCTGTATTTCGAGGGCCAGGAGAAAGCACATAATCAGGACCTGG
Seq A exon
GTAGGTAACTGCTGTCAAGGCTCAACTCAGTTCCCAGGCTCGCTCATGGTGACTACGGGAGCCCGAGCCCCAGTGACAAGCCTCTCTCAGGCCACCTTCTCCAGGCCTCGGAGAGACTGAGACAGATGGCCATGGAGACTTACTACACCCTCAGCCTCAGGCTCCCCACATAGGGCCATAGCACCCATGTCTCATGAGTTAGTCTAGCTGTGCACCACCCTCCCCATTGGAGGCTCCAGTTGCATTCACGATTCTCTTGCTTTTTGACCCAAACCTAGGGTCATGGACTTAAATACATTCTTCACACAGACACAAAGCAAGCAAACAAACAAACAGGCGTGTGTGCGCGTGTATACACGAGTGCGTGCTTGTGCATGTGTGCATCTTTAAAGGACATGAACATGACGTCAAAGAGTTTAAAAAAACTACAAAACACACATGGTAGAAGTGGGCAGGTGTCTCTGCCTACCATCCCTCAGAGAGCCAAAGTGCCCATGGGAGGCTGGAGTATTTATGTCAGTGTTGGTGAGAGCAGGGCCGTCAGCTCCTGGAAGTGCGGGCATTCCTGTCTGTGGCCTGTTTCCCACCGTAAGTCTTACAACGCAGTGGAGAAAGGACAAACAAGGATAGGACCCAAAATAGCTGTAGGATCCGGGGATGAGGTCTGGCCTCGGCCCCTGCTGGTTTGCTGAGGGTGGACCCTGTCTGAAAACTCCTCAGTATGAGAAGGAACACCTTGCCCCTGACCAGTTCTGTGCCTCATGGTCGCTCGGCTGAGGTGGAAGCGGGGCTCTATTCTTGTGTGTTCTTCACACAG
Seq C2 exon
GGCTGGCGGGCTCCTGCCTGGCACGCTTCAGCACCATGCCCTTCCTGTACTGCAATCCGGGTGACGTCTGCTACTACGCCAGCCGCAACGACAAGTCCTACTGGCTCTCCACCACGGCCCCACTGCCCATGATGCCCGTAGCTGAGGAGGAAATCAAACCCTACATCAGCCGCTGTTCGGTGTGTGAGGCTCCGGCCGTGGCCATTGCTGTCCACAGCCAAGATGTCTCTATACCCCACTGCCCCGCTGGGTGGCGGAGTTTGTGGATCGGATATTCATTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.262 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(37.3=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGCTCTGGAGTGGGTACA
R:
TATCCGATCCACAAACTCCGC
Band lengths:
343-1160
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]