RnoINT0039876 @ rn6
Intron Retention
Gene
ENSRNOG00000018951 | Col4a5
Description
collagen type IV alpha 5 chain [Source:RGD Symbol;Acc:1565499]
Coordinates
chrX:112920265-112921811:+
Coord C1 exon
chrX:112920265-112920433
Coord A exon
chrX:112920434-112921718
Coord C2 exon
chrX:112921719-112921811
Length
1285 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
ACCAATTCATTTGTTTTCAGGTC
3' ss Score
9.59
Exon sequences
Seq C1 exon
GGTGGAATCACTTTTAAGGGTGAAAGGGGTCCTCCTGGGAACCCAGGTTTACCAGGTCTCCCAGGAAATATGGGACCTACAGGCCCTGTTGGTTTTGGGCCTCCAGGCCCCGTAGGTGAAAAAGGCATACAAGGTGTGGCGGGAAATCCAGGCCAGCCAGGATTACCAG
Seq A exon
GTATGTTTACTATTGTTTTGTTTTAAAAGTAGAAATAAGATATATATATATATATATATATATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGGCGGATGGATAAAAAGTTAAAAAAAATCTTGGGAAATGTGTTTCTTTGGCCATCTATATGTTTATAGGAAGGGAAGACAATGTTTTTGTTTAAAGTGAGATTTCTTGTTAACTTATTCCAGCCAATGTTGATAGTGTTATTTGTATTTTGTTCTTGTATACATGTTTCTGTAGCTGTATCTATGTAACTGGAAAGTGTTCATGCACATAACTGTTTTTATTAATATTTTTAAATTATAATAGAATTATAAAATTTTCTGCCTTCCTTCCTCCCTCCAACTCCTTCCATCTCCCTTGCTCTTTCAAATTTAGATCCCTTTTCTTGAAATGTTGTTTCATATGTGTGTGTTCCTATATGTACATTTCTAAACACACACACACACACACACACACACACACACACACACACACACACACACACACGTACCTGAATACATAAAAACAACCTGCTTGGCCTGTATAATCTTACCTTTATGTATATGTTTTGAGGGCCAAGCACATGTACCTTAATTTTAGAGAGAGGGTCCCTCACTGAACCTGGAGTTTGTCGTTATCACTAGGCTGACTAGCCAGTGTACTCCGAGGGTCTGCTTCCCTCCACATGCTCAGTATTTGGGTTATAGATGTGCGCTGCCATGGCTACAGTGTTATGGGTGGTAAGGATCTTACTACAGATTCTTAGTCAGCAGGCACTCTGTGGGGAGCTACCCTTCCATCCTAATTTATGTTCTGAGTCTCAAGGTAGTTGTTCCAGATAAAATTGAGAGAGATTTTCCTGTTTTTGTTTTTGTTTTTTTTTTTTTTTGTCTTGTACTATCCATGTTCTCTTGTGTTAGACGATAATGGCCCATATTGTACAAAGGCAGACCTCTCCCTTCCTTAAATCACTAATTTAAATACACTTATCTTCTGCAATTAGGGGCCACCGGCATAAAGCAGAGATATTTTATCAGCTTTCTGAATATCCTTTAATCTAGTCTGGCTGACATCTAAAATTAATAATCAAATCATCAATCATGGAAGTACCTAAAAGCATCATCTGCTTTTAATCTTTGAAATTTCTTGTATAGACAGAGTGGGATCGTTATCATTAGTCAAGTCTCTGATTCTCACTGAGACCAATTCATTTGTTTTCAG
Seq C2 exon
GTCCTAAAGGTGATCCAGGCCAGACCATCAGCCAGCCAGGAAAGCCTGGCTTGCCAGGGAATCCAGGCAGAGATGGTGAAGTGGGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018951:ENSRNOT00000064478:25
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(14.0=12.3),PF0139113=Collagen=PU(85.0=89.5)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=25.0),PF0139113=Collagen=PU(44.7=65.6)
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:
GGTGGAATCACTTTTAAGGGTGA
R:
GACCCACTTCACCATCTCTGC
Band lengths:
256-1541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]