RnoINT0039879 @ rn6
Intron Retention
Gene
ENSRNOG00000018951 | Col4a5
Description
collagen type IV alpha 5 chain [Source:RGD Symbol;Acc:1565499]
Coordinates
chrX:112923182-112924898:+
Coord C1 exon
chrX:112923182-112923279
Coord A exon
chrX:112923280-112924747
Coord C2 exon
chrX:112924748-112924898
Length
1468 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGA
5' ss Score
4.3
3' ss Seq
TTGTCATGTGTATGCTTAAGGGA
3' ss Score
4.38
Exon sequences
Seq C1 exon
GTTTTCCAGGAATTCCTGGACCTCCAGGACCTCCTGGGGCCCCTGGAAGAATGGGCCCAGAAGGGCCTCCTGGGTTACCGGGCTTTCCAGGACCCAAG
Seq A exon
GTCTGAAAGTTATTTTTAAAGGATTTATTTATTTTTACTTTGTACGTGTATGAGTGATTTGTCTGCATGAGTATATAGGTGCACCATGGGTGCCTGGTGTGATGACTGTGGAGGTCAGAAGAGGGCCTCAGATGCCCTGGAACTGAGGTCACAGACAGTTGTTAACTACGGTGTGGGTGCTGGGAATCGAGCCTGAGTTCTCCACAAGAGCACTCAACTTCTGAGCTATCTCTCTAGCCCCAGTCTGGAACATTTTACCTTACCCCTTTCCATTTTTCCATCTTCTCTACTCTCCTTAGTCCCAGTTCCTATTCATCTTAGACATTACACCAAATCTTTATTATATTGATACATAGCATATTTTCATTTAAAAATAACAAATCCCAAACCATCTTTAATACGATAAGAGTTAATACTTAGATCCAAAAAGTTTCTGACCTTGTGTTAGACTGGTAGGTTTTTGGATTAGATGAAAGACCCCAGTGATCAGCTTGGCCTATGTTTATGTATATAAACAATAACTTATTTCATACTTACAGTACATGTGTGATGATTGGTAAAGTTGTGCTGGATATATCAAGCCCTTCCTGTATTCTTTCCTCTGTTCCAATTCCATTAAGGATACATAAATCAAATCCCTGCTACTTGGTAGTACTAATAAGTAACTTCCTTTATATTTCTTCTATTGTATCTTATTTAACCTCTAACACTTTTCAGTCAGCCTTCAGCAGAGTGCTGCAGTGTGTAATTATCCCAACCTTTCCTGTATCTTCTGTGCTTAAATGATTTAATCTCTCTGGGTTTCATTCTTATTACTTGTTTTTCTTGGGGAAAACATCTGATAGGCTTTCATGAGAAAAATATATCTCTGTTGGCCTGCTTTTATTTTATGATGAGCATTTTCAAATAAACACAGAAGCCAAAGAAATAATGTAATGAAATTTCACATATGCATTTGCCAGGTACAAAGTGACTAAGATTATAGTAACACTTCCTTGATCTTTTCCTGTTTTTTGGGAAGTCTCATTTAACCCAAATCTCAAAATTACAACATTTCACTTACAAATGCTTCAGCATTCAGATCTAACTAAATGGAAATTGTATACAGAAACCACAATGGCATTATAAGACTTAGTCATGTTAAAAATAATTACACGAATTATTTAATTCTCAGTCCACATTCACGTTTCCTCAAATGAGTAGAGTGTCATTTAATCCTTGGATTTTCAGTTAACTTTCATATTTTGAAAACAGTCCAACTCATTTACTTTGCTTTTACTAAATTCTATTTCTGATCCTTTCAGATATTTTCTCTAACATGCCCATTATTTTTAATTTAATTATCCTCTCCTTACTATGGAAGAGAAATATTGCTTTGTATTCAATGCTTTCGATTCTCTATAGTAAACTGTAAACACCAGGAAAGTCACGGGACTTTTCGTTGTGTTTTGTCATGTGTATGCTTAAG
Seq C2 exon
GGAGAGCCAGGATTTGGGTTACCTGGGCCACCTGGGCCACCAGGATTCCCAGGTTTCAAAGGAACACCTGGTCCAAAAGGTGATCGTGGTTTACCAGGACCTCCAGGTCCTCCAGGACACACTGGCTTGGATGGGCTACCTGGACCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018951:ENSRNOT00000064478:28
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(55.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(24.1=27.5),PF0139113=Collagen=PU(70.1=92.2),PF0139113=Collagen=PU(9.5=11.8)
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:
AGGAATTCCTGGACCTCCA
R:
TTTGGTCCAGGTAGCCCATCC
Band lengths:
240-1708
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]