RnoINT0039875 @ rn6
Intron Retention
Gene
ENSRNOG00000018951 | Col4a5
Description
collagen type IV alpha 5 chain [Source:RGD Symbol;Acc:1565499]
Coordinates
chrX:112919204-112920433:+
Coord C1 exon
chrX:112919204-112919395
Coord A exon
chrX:112919396-112920264
Coord C2 exon
chrX:112920265-112920433
Length
869 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
TTAAACATTTCCATTTTCAGGGT
3' ss Score
10.87
Exon sequences
Seq C1 exon
GGCATTCCTGGACCTCCAGGTGCTCCAGGCTTTCCAGGGTCTAAGGGTGACCCTGGTGATGTTCTCACTCTTCCGGGAATGAAAGGTGAAAAAGGAGAATTGGGTTCCCCTGGAGCTCCAGGGCTTCCTGGTCTACCTGGTAGTCCTGGAAAGGATGGTTTGCCAGGACTTCCTGGCCCCAAAGGAGAGCCC
Seq A exon
GTGAGTTGGTTTGATATTCTTACTTTTATGTCAGATTGTCATTTAGTAATGTTTCCTACAGCATGAGTTTCTATCTCAATGGTAGAACTTATACTTGGTGTGTGTGAGTCTCTCAATTCAATTCTCAGTACTCCCCACCCTCCAAAAAGCACTTGCCAAATTAAAATAGAAAAGGATCCTTGTTATTAGATGAAGATTCTACTAATGCCTAAAATCATATGATTTTACATTGAAATGGTACATCGATACTAACTACAATTGTTTTACTGTTTTCTTTCAGTTTTATCAACGCAGTATGGTATTGATTATTATTAGCTATAATTAGATGGACAGGAAGATAAAATGCTTAGGTGTCAGTAAGATTCAGCTCTTATTCTAAACATCTCTGTGATCCTTTAAGCATGAAAAGAAATCTAGTTTGCTTTGTATATATAGAAATGTTATAGATTTCTGTGAGTAGACAGCCAGATTAAGAATCTAAAGAGTAAAACACTAAGCATAAATATTCTCTTTTATATTCAACATATAGTACAGGGTTTTTGGATGGGATATATACATATATATTAATAGTATTAATAGACAATAATATCTCAACTCATGGTAGGGTATAACATTTTTGAGAGAAGAGACTTTCATCTACTCGTCTACTCAGCTTGTACCTCTGAAAGATAGAGTTCAGAAATATTTACTGGAGCAGGGAATGAGTAAGTAGGTAATCATAGACTCAGTTTAAGAACATCATAACACAGTTATATAGCATAACTTCAAGGAGTATGGCTGGATCATGTCCCTGGTTGTATTCATTCATACTAACCTACATGAAGTTGTTACCATCAATGTTTTTATGTCTTAAACATTTCCATTTTCAG
Seq C2 exon
GGTGGAATCACTTTTAAGGGTGAAAGGGGTCCTCCTGGGAACCCAGGTTTACCAGGTCTCCCAGGAAATATGGGACCTACAGGCCCTGTTGGTTTTGGGCCTCCAGGCCCCGTAGGTGAAAAAGGCATACAAGGTGTGGCGGGAAATCCAGGCCAGCCAGGATTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018951:ENSRNOT00000064478:24
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(31.7=31.2),PF0139113=Collagen=PU(82.0=64.1)
A:
NA
C2:
PF0139113=Collagen=PD(14.0=12.3),PF0139113=Collagen=PU(85.0=89.5)
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:
CTCCAGGTGCTCCAGGCTTTC
R:
CTGGTAATCCTGGCTGGCCT
Band lengths:
348-1217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]