RnoINT0039883 @ rn6
Intron Retention
Gene
ENSRNOG00000018951 | Col4a5
Description
collagen type IV alpha 5 chain [Source:RGD Symbol;Acc:1565499]
Coordinates
chrX:112934667-112935891:+
Coord C1 exon
chrX:112934667-112934834
Coord A exon
chrX:112934835-112935801
Coord C2 exon
chrX:112935802-112935891
Length
967 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
GTACCTGATATTTTCCAAAGGTG
3' ss Score
6.75
Exon sequences
Seq C1 exon
GCTTACATGGAATACCAGGAGAGAAGGGAGATCCAGGACCTCCTGGGCTTGATGTTCCAGGACTCCCTGGAGAGAGAGGTAGTCCAGGGCTCCCTGGAGCCCCTGGTCTTATAGGACCTCCAGGATCACCTGGTATCCCTGGAAGAGCAGGTGTCCCTGGATTTCCAG
Seq A exon
GTAATGTTTAATAATCTGTCTGACTATGGATCAATTAAACTAATATTAATATGACTGACAAATAATTTTCTATTGCATTTTATGAATTGATACTATCTATTAAGGAAGAGTGTTAAGGGTATGAGTGTTAGAAACTCCATTGGTGTTTTCACTATAATTTTTAACCATGTGACAATACCAGTTATATATTACTATATAACAAATGATCCAAAATATGATGGTTTAATGTAACTTTTCAAACATTTTGCTTAAGATTCTTTGGGTCAGAAATCAAAAGGTGCTTTTAACAGATTTATTTCTATAATTCATATGACTCCAGTGAGCATGATAAGAGTTGAAGAATCCAACTCTATGGTGACACTCTCCTGACACTTGGGCATTCTTTAGCTCATGTGACATCTAATGATTCATAATGCTTCTTCTCATCTGTTTATCATCCTTCCATTGCAAGCGGCTTCCCAAAGAAAGAATTTCACGGTTAAAATCACTGGCTATTCTTTCAGAGGACTGTGGTTGGATTCCCAGCTCTCACAAGGCAGCTCCCAACTGTCTGTAATTCCAGTCCCAGGGGATAAAGTGCCCTCTTCCGGCCTCTGGGAGTATACATGCACATGGCGCACCGCCCAGACCTACTCAGCCAAAATACACATACACATAAAATAAAGATAAAAATGTGCTTTCTGGGGGTGGGCAGAGTGGGGGAGAAGGGAAGGAAGGAGGGAAAGAGAGATGGGGGGCAGAGTTAGTTTCAGGGCACCTTGGTTAGTGAATTTTCTTATGTAGCCTTGGGAGTGAGTAACTATGAGTTTTGTTCAGGAATGAGGGCTAAGCTTACAGAAATAAAGGGTAAAATCTCACTGTGCTTTCCTTTCATTCCTAAATAATTTCCCGATTGATACCTTTACAAGTCCATCTTATCTTTCCAAAGTCCAAAACCATGAAATTTAGTACCTGATATTTTCCAAAG
Seq C2 exon
GTGTCAAAGGCGAAATGGGTATGATGGGACCTCCAGGCCCACCGGGACCTTTGGGTACTCCTGGCAGGAGTGGTGCTCCTGGTCTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018951:ENSRNOT00000064478:31
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(28.6=31.6),PF0139113=Collagen=PU(65.0=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(33.3=64.5),PF0139113=Collagen=PU(42.9=87.1)
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:
TGGAATACCAGGAGAGAAGGGA
R:
TTAAGACCAGGAGCACCACTC
Band lengths:
249-1216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]