RnoINT0039766 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83409651-83411432:-
Coord C1 exon
chr16:83411326-83411432
Coord A exon
chr16:83409853-83411325
Coord C2 exon
chr16:83409651-83409852
Length
1473 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGC
5' ss Score
8.8
3' ss Seq
TAACTGGGATTCTCTTGCAGGGC
3' ss Score
8.42
Exon sequences
Seq C1 exon
GTGAGCGAGGACAGCCAGGTATCCCTGGTGTGCATGGGATGAAAGGTGATGACGGTGTCCCGGGACGTGACGGGCTGGATGGATTCCCTGGCCTGCCGGGTCCTCCG
Seq A exon
GTAAGCTGTTGCCTCACTGCAGCTCACCCAGCCCCACTCCTCAATTCCTTCCTGTTCTTTGGACATTGGAGGGGTCGTGGCCTTGACCTTGGCTCTCCCCCAGTGCTCAGGACAGGTCTATTCTGTTTCGGTCAGGGATGTCCTGTTTTTAGAGACTAGTGAGTAGAGTGAACTGTGAAGCACAATGAACGCTTCAAACAGTGGAGTAATATCCATTGTGGTCTCTGTGGAGTAAGACCCATGTGTTGTCAGGAGAGGGTCTTCCCTGTTCCCAGGCAGCCCTTGGAGAATTAGTGTCCTTTGGTGTTCACAAACCTCGAGTGTGCATGCTCTAGCAAGCTAGAACATAGTGTTGTAAGGTGAGAAAAAAAATGGCTTACCCATTTTGGCTTGCCCACGTGTTATTCACAACCAAAGTTTGTGTTGTCCACTCTATGATCTCCGGTGGCCATCTAAAAGGGGGAGTCCCGCTTTGTTGACCCCACACATACTAGAGAGGCTAAAATATGGAAGCACACGTGCTTTAAGAGTCCTACAAACAAAGAGAGCTTGACCCAGTGACTTCCTGTAATACTCTCTTACCTTTGAATGCAAAGGAGAAACTGATGTCTGAGCAGGCTGACTTCTCAACTCCTGCCCACCTGCCATCAGAAGTACCCTTCTCCCTCTTGATTCCGTAGGCATGCTAGGACACCCAACATCTCATTAGCCAAGTGTAGCACTGACACTGGATCCCTTGCTAGGTCCTACCATATGAGCACTGCCCCTGCCTACTTCCAGCACTCCCTACCGGTGTTTGTGTTTGTTTGTTAAAGATTTATTTACTTTATTTTTTTATTTATGTATATAAGTAGCTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGGCACCATGTGGTTGCTGGGAACTGAACTCAGGACCTTTAGAAGAGCAGCCAGTGTGCTCTTAACCCCTGAGCCATCTCTCCAGCCCAGCCACTCCCTACAGTCATCCTTCCATTGCTCACCCTAGTAACCCTACCTGGCAGGAATCATCACCACGAGGCATGGCCACATGGACAGGACACCTACCTGTCCCCATTCTAATCCTGTAGATGCCCCTTATTCTAAGAGCACATGGCTCTTTCTCATCTAATTAGCTCCCTTCCTCTAATGACCACACGTCCCTCCTGAACAGCAGACATGCCCACATGCTAATCCTAGCAGGTGGACTGGAATTCCTGTGCCCAGGGTCCTGAATATAAATGTGTGTCTCCCGGGCTGACCCTCCACTGTGCTGAAAGGTGGTGCTGTGAGTCCTAACTTCGACTCGGCCGCTTGCATACACGTTTTTCTCCCAGCTCTCCTGTTCTTGACCGCGGGATTCCAGAGAAATGGGGAAGGGAAGTCGGGAAGACACAGCTGGCTCGGATGTCTGTATATGTTTGAAGATAACTGGGATTCTCTTGCAG
Seq C2 exon
GGCGATGGCATCAAAGGGCCTCCAGGGGACGCAGGTCTCCCTGGCACACCTGGAACCAAGGGCTTCCCAGGAGAAGTGGGTCCTCCAGGACAGGGCTTACCCGGCCCGAAAGGTGAACGTGGTTTCCCTGGAGACGCCGGACTGCCTGGACCTCCAGGCTTCCCGGGTCCTCCAGGTCTCCCAGGAACACCGGGTCAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:21
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(50.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(42.9=44.1),PF0139113=Collagen=WD(100=97.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCGAGGACAGCCAGGTATC
R:
TGACCCGGTGTTCCTGGG
Band lengths:
302-1775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]