RnoINT0039894 @ rn6
Intron Retention
Gene
ENSRNOG00000018951 | Col4a5
Description
collagen type IV alpha 5 chain [Source:RGD Symbol;Acc:1565499]
Coordinates
chrX:112964678-112966807:+
Coord C1 exon
chrX:112964678-112964811
Coord A exon
chrX:112964812-112966734
Coord C2 exon
chrX:112966735-112966807
Length
1923 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
AATGATTTTTGTTTACTCAGGGT
3' ss Score
7
Exon sequences
Seq C1 exon
GTCCACCTGGTACAGAAGGTCCTCGTGGCCCCCCTGGAAATGGAGGTATTAAAGGAGAGAGGGGAAATCCAGGTCCACCTGGGCAACCAGGCTTACCTGGCTTGAAAGGAGATCAAGGACCACCAGGCCTTCCG
Seq A exon
GTAAGAAATGAGACTACACATTTGATGGTAGAATAGAGTGGCTGACAGCTTTCGAAATGGGAATTCTGAGCAGCAGAACTTTGCTAACACTCACCACATGGCTCACTGGTGAAGTAAAAAGAAGAGTAGAAGGCAAGGTTCCTAGTCTTCCCACTAAAATGTCTTTGCTGTTTTATACTAAAAGAGTTTTGGTTAGAACAAACCTATGAAAAGGAAACTTACATATACACATCAGTACACTGCATTTGGACGGATACACCATAGGAGAGTAATTATGGTGAGTGGGACTAGTTCCGACTTTGAAATTAGAGTCAAGGTGTAGTCTCAGTCATACTGTTTCTCTAAGTTTAAGTTTAAGTTTCTCTCTTATATAACCACAGTGCAGCTATCAACTTGACAAAATTGAATAGAAATCAAATATTTTAATTTCTACTATCTCTGTTCTGATTTTATCAGATGGTATAGTAATATAGATTTTAACATTTCATCCTGTAGCAAGGTATCTGGACCAAATCATGTATTCCACTTAACTGCTGCGTCTCTTTATTCTATAATATGAAATAGTTTCTTAGCCTTTTTTCTTTCATGACTTTAATACATAAAAATGTAGCCTCTCCTCACTTTAAAAATAGAATAAGCCTTCCTTTGTCTAATTTGTCATTTTAATCAAATTCAGGTTATATAGCCTTAGCTAGAATACTATAAGAGCAACAAAAATACTATCCTCATCAAGATTTCTCCATAAGTTTAACATCTATTAATGCGTTTTGAATGGAAAAATTTTACTGGGTTAATGGCAAAAATGATGACTTTGTAGACTCCGCATTATCTCCACATGTACCATTTAGTCCTACTGTAGGCAAGAGATGTCCCTTCTATTCTATGCAGTCACATATTTATTATGAGTATGGACTCATGGTTTTTTCCCAATGATTTATAAATTTTTAAACTGCCATTGCTTATTTTGCTATTCACATTTTTCCAGATAGCCGCATGGAGCTGGATCTGCTGGCATTCTGACATGCTTCTAAAACCTCCTTTTCTTTGACACTTTCCTATATTTTGACATAAAAATACATTCTCACCTTAGGCCCTTTTCAGTCCTACTATTAAAGGCTTCATAGTCCTACAGTTAGTGCAGTACTGAAGCCTCTTGAATCATTTTGACATTATGTGTGCTACCTTTTAGATTCTTGAGCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTTTGTTGCTTCTATACTATCAGTGGCTCCTCAACCTATTATAGTTCCTATATTATATTTGCCAAGTCTTTTTATAATTTCTATACAAATGATTCTAATCTAAGCATCTATCGCCTCAGATCTAGAGTAAAAAGAAAGTGATCTTTTTAATAACCATTACTGACTAAATATTCTATTATCAACTATTTCCTAAGCATTTAAGAAGAACTTTGTCATTTAATCTTTACTGTCACTCCATAAAGTAGGCCTACTACTATTTTCTCTGTGCTGGGTAAAAGGTAATAAGCAGACTGAGAATTTAGATCCTTCCAGTTTAACTGGAGCAACAGCTCTCTATGCTACCATGCAATACTTGAATATTTTTCCCATTTTTTAATTGGGCATTTTCTTTATTTACATTTCAAATGTTATCCCCTTTCCTGTTTTCCCATCCATAAGCCCCCTATCCCCCCTCCCCTTCTTCAATAAGGGTGTTCCCCCACCCACGCACCCCTTCCTGCCTCCCCACGCTGACACTCCCTTACACTGAGGGTCGAGCCTTGGCAGGACCAAGGGCTTCTCCTCCCATTGGTGCCCAACAAGGCCGTCCTCTGCCACATATGCAGCTGGAGCCATGGGTCTACTCTGTCTTAGTTATGTTCCTAACAGCAATGATTTTTGTTTACTCAG
Seq C2 exon
GGTAACCCTGGCCGACCAGGTCTTAATGGAATGAAAGGAGATCCTGGTCTCCCTGGTGTTCCAGGATTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018951:ENSRNOT00000064478:44
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=PD(57.4=77.8),PF0139113=Collagen=PU(45.2=84.4)
A:
NA
C2:
PF0139113=Collagen=FE(28.6=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:
TGGTACAGAAGGTCCTCGTGG
R:
CTGGGAATCCTGGAACACCA
Band lengths:
200-2123
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]