RnoINT0039703 @ rn6
Intron Retention
Gene
ENSRNOG00000016281 | Col4a1
Description
collagen type IV alpha 1 chain [Source:RGD Symbol;Acc:1307148]
Coordinates
chr16:83587665-83589233:+
Coord C1 exon
chr16:83587665-83587727
Coord A exon
chr16:83587728-83589197
Coord C2 exon
chr16:83589198-83589233
Length
1470 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TAAAATGCTGTCTCTTACAGGGT
3' ss Score
10.51
Exon sequences
Seq C1 exon
GGCTCACCAGGGTTGCCAGGACTCCAGGGACCTGTCGGTCCTCCGGGATTTACTGGACCACCG
Seq A exon
GTGAGTTCCGAGGATAGTCACGTGGAACAAATTGAAGCTGACTGAGACTCTTGCCCCTTGTGGCTGACAATTCCCAGAGCTGTGGGAAAAAGATGCTTTATATGGTGGACCCTCAAGACATCCTGGGACAGACCACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAGGCAGGAGGAAGCTGGACTGAGGGTCACCAGGGTGGCCCCTGCCGTTTGTGAGGAAGAGAGCTGCTTCAGAGGCAAAGCCTCATCACAATTTAAGGGTCCGTTAGGAGCCAGGCACAGACCTGGGGAAGACGCTGAGATGGACTGGGCGCCTGCAGGTGGCGCTAGAGAGGAAGGCTGCCCCGGACTCTGTATGACTGACATTCTTAGCAGAAGGAGAGACACTTCTCACTCCCTCATTTTGACAGCAGTGAAAAGACTTATTTACTAAGAATCAAGCGTGCAAGGAGAGGGGAGAGGCGACTGAGCTCGTGGCCTGCACACAGCCTGCCTAAGCATCTTCTCAGTGAGCTTCAGGCTTATTCCTTAAATTCAGTCTTTTTCTATTGTTTTTCTCCACATATGGGAACAGAATCCACTCACCTTCCGATGGATCAATAGGCTTTTCTTTTTTTCCTTTCTTTTTTTTATTTCAGAATGGCTGTCTTTTTTTCTTTTGAAAAAGTGATTATGGGATCTGAGATTTTCTTGCAGATGTGGGGCTATCTTTTTGGTGTCAGCAAAATCTACTCTCCAAAAGAATCACTTTTTCGAGGTCTGAAGTGGACAATATTGTCCTCATGTGGGCAACTCCAGCTTGGAGCCTAGGCTGGTGCCTCCAGGTTACCGGTACCTAAGGGACAGGCCGCAGCCTTTGAGGGATTTCCGCCCCTTCTCGTAATTATCCTGATCCATAGAGGGCTGTTTTCAAAGCTTTATAGGTATGTGTCATACACATCATCCTTAATACATACATGTCCACAGCACAGAGGACTGTGTGTGTCAGACTTCCTTAGGACACAAATCTTCAAGGCTACAGTTCGCAAGGAGGAAAGATTCATCCTGGCTCACAGTTTCAGGGAGTTGAGTCACATGACCCTAGGATCTGTAGTTTCAGAGCCTGTGGGGAGGTAGAACACTGTGGTGGGGAGCATGAGGTATAGTTGAGGCATACAGAGGAAGAGGGGGAGTTTGGGGGGACAAGATGCCTCCTTCAAAGGAACAACTCTAGCGCCTCATCCTCCAAACCCTCCCCTCCCCGACCACAAGAATGGTTAGACACCCTGGTGATGCAGTCACTTCCTAATAGCACCACCAGCTGGGGAACCAAACCTTCTACAAACCCCGTGTGCATTTGTGCGTGCATGTGTGCGTGCGTGTAGGCGTAGGAATGATCTTCCAGATCACATCTGGCTGGTTTTGAATATCATTTAATTAAAATGCTGTCTCTTACAG
Seq C2 exon
GGTCCTCCAGGCCCTCCTGGACCTCCTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016281:ENSRNOT00000057386:10
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(33.9=100),PF0139113=Collagen=PU(12.5=38.1)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=100),PF0139113=Collagen=FE(17.2=100)
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:
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]