RnoINT0039941 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112408645-112411096:-
Coord C1 exon
chrX:112410980-112411096
Coord A exon
chrX:112408837-112410979
Coord C2 exon
chrX:112408645-112408836
Length
2143 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
ATATGTTCTTTTCTTCTCAGGAG
3' ss Score
9.1
Exon sequences
Seq C1 exon
GTTCCAAAGGCCTACCTGGCATCCCTGGCAAGGATGGCCCTAGTGGGCTTCCAGGCCCATCTGGAATCCTTGGTGATCCTGGTCTCCCTGGACTACAAGGACCTCCAGGATTTGAAG
Seq A exon
GTCAGGTTAACACAACTTGGGTATTTAGTCAACCATGTGGTAAATTTGCCAGTATGAGGTAGCTCACAGGCTGAGTTCTTGTTTCTCTTAATGTTCTATTACTATGAAGAGACACCATGACCAAGACAACTCTTATTAAAGAAAGCATACCAGGATTGGGGTATTCCTGTGACAGGCCTGATCATGCTTTTGTTGTTTGGGACTTTGGACTAGAAAAGTGGTTGGATACATTAAGCAAGGATTAAGGAGCCATAATAACAAGAGCATAGAAGACAGTATTGAGGGAAATTTGAACTTTGGGGGTCTGGCTGAAGAAATTTCAGAGGGGAAAATATTGGTAAATAGGATAGATACCATTCTTATGATATATTTGACACAGAATGTGGCTGCTTTTTGCCCTTCCCATAAAAATCTGCCTGAGAATAAACGGAAGAGTTTTGGATTAATGGTGTGGGCAGAGGAAATTTCAAGATAGCCTAATGTTGACTGTATTGTGTGTTTTTGATAACTCTTATGCAGATCCACAATGAAAAGGAGCAGGGGAAAGCAAGGAAAAAATACAAAATGTACAGTTTGAAAAGGAGCACCAGGAAAAATACAAAATGTGAAGTTTGAGGAGAAAGGGAGTACCAGGAAATGTTCTGTTGGAGTCAATTCTAGTGCTCAAGGAATAAAAAACAATTAAATCTTGCTGCTAAATAAAATAAAGGGAGTGACATCAGGGCAAGACCCCACTTTTGGTACCATCTTATGTCTTTCTCACTGTTCTATTGCTGTGAAGAGACACCATGACAAAGACAACTCTGAATAAAAAAATAATGTAATTGGGGGCTTACTTGCAGTTACAGAGGTATAGTCCATTATCATCCTGAATGGAACATGACAGCAGGCAGGTAGGCACACACTTTCTCCAACAAGGCCATACTTCCTAATCTTTCTCAAATAGTGGCATTCTTGATGACTGTCTTAGTTAGGGTTTTCCTGCTGTGAACAGACACCATGACCAAGGCAACTCTTATAAGGACAATATTTAATTGGGGCTGGCTTACAGGTTCAGAGGTTCAGTCCACTATCATCTAGGCAAGAGCATGGAGGCATCTAGATAGGCATGGTGCAGGCAGAACTGAGGGTTCTACATCATCTGAAGGCTGCTAGCAGAATACCGACTTCTAGGCAGCTAGGATGAGGGTCTTAGAGCCCATACCCAGAGTGCTACAATGCCTCCAACAAGGCCAAACCCACTCCAACAGGGCCAAACCTAGGCTGAGCATATACAAACTCTTACACTAAGCATTAGGCTATATGAGCCTATGGCACTTATTCTTATTCAAACCATTACATTGTTCTTCTACTCTTCACACTGCACAGCCTCCGACCTATGAAGGGAAGTCCTACATGATTCAAGAAGGCAACAGACTTCTCCACATCATTGTCTGGGTTATCCTCCACCTTTCTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATGCATTACCAGTGTCTTGTTGCATAGCCCAGTTTGCCCTCAAACTCACTATGTTATCCAGGTTGACTTCAAAATCTTCCTGGTTTTCCTTTTTATGGCTTTCTGTCCTATCCTGACATGGATGAAAGAATACAACAAAATCACTTGTCCTTAGTACAGAATACTTCTAAAGCTCAGTAGTAAAATGTTACAGTCATATCTACCATGGACAAGAGAGGCAGATGAAGCTTTGTCCGTCTAATGCTAATGTTATTTATAATGCTTCTGATTCAGAAGCTAGTTATGCCCTGTGAAAGACTTCAATGAAGGCTGGTCATGAGAAGAATTCCACTCCATTCACTCTTAGAACAGAAGGCCAGTCTGAAGAAGGATAATGGATGGTAGACTCTTGAAATGGGAACCAAATAGCTGGGCACACATGAATTGGACTTGTAACTCCATTAGCGTCTAGTTGTAGCAGCTCAGAACCTCATTTTCCTCAACTGTAGAGTAGGCTGATAATAGTGCCAACTCCTGGGGACATCAGAATCAAGTGGTTGAACACCTGTATATGATGTGCCTTACAAATGTTTAGGATCAATGAGTGGCTAGTGTTATTAGCATCTGCATCATACTTACTTATATGTTCTTTTCTTCTCAG
Seq C2 exon
GAGCTCCAGGAAATCAGGGCCCCATTGGGCAGCCTGGGATGCCTGGACACAGTGTGAGAGTGGGCTACACATTAGTAAAACACAGTCAGTCAGAACACGTGCCACCATGCCCCATTGGCATGAGCCAGCTATGGGTGGGTTACAGCTTGCTGTTCGTGGAAGGGCAGGAGAAAGCCCATAACCAGGATCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:40
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=0.477
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(44.1=65.0),PF0139113=Collagen=PU(60.0=90.0)
A:
NA
C2:
PF0139113=Collagen=PD(38.3=35.4),PF0141314=C4=PU(40.6=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]