RnoINT0037146 @ rn6
Intron Retention
Gene
ENSRNOG00000060460 | Clec1a
Description
C-type lectin domain family 1, member A [Source:RGD Symbol;Acc:1566110]
Coordinates
chr4:163200606-163202073:-
Coord C1 exon
chr4:163201975-163202073
Coord A exon
chr4:163200783-163201974
Coord C2 exon
chr4:163200606-163200782
Length
1192 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGT
5' ss Score
7.65
3' ss Seq
GACTCTGTCACATGACTTAGTTT
3' ss Score
3.44
Exon sequences
Seq C1 exon
AGAATGGGACACCCTCTTCAGTTTGGCGCCCAGTGGCCCTGACCCTGCTGACCTTGTGTTTGGTGTTGCTCGTTGGCCTGGCAGCCCTGGGCCTTGTGT
Seq A exon
GTAAGTCTGTGCTCTACCCTGGGGAAGGTTCTTGCTATGAGTTTCTTAAAACCTTAGTTCTCGAGTCCCTTCATCTTTCTAAAGGCAACTGTTTAATTGACTAGGAGTTGATGTAGTGAAATAAAGTGAGCATTTTCCTGTTAAAGGAAAATGTTCTTTTTGAGATAAGTATTGTATCTGTTTATATGTTGGGGTGTAAATAAGTACTTTAGAGAGCACCAGCAGTGTAGGAGAATGTGGCTTCTATACACATCCAATTTCTACACAAGGAACATAAAAGTGCTCAATCACGATTGTCCAAACGACTGGCAAATAATAGTTATTTAAGGGGGGGGAGTATGAAAATCAAGCTAGGAAGATTGCATGTGTTATACCGTTACATTTCAAAGCTGCAAAGGTAAATTTCTTGATGGGCTCTGGCAAATTGGCTTCATTTGCTAAGAACATACAGCCCCTTCCTGAACTGCTGAAGGTGACTCGGAGCAAAAGCCACACAGTAAAGTAGATCAGGGCGGCAAGGGGATTCTGCTAAAGTCAAAGTTAAATCTATGAACTTCACTTTAAAAGTTAAAAAGAAATTCTGTTAGCTCTCTTTACTCCCGAACTTACATAGTCTTGATAGAGCACTGTCTAGGAACCACCTTCTTTCCTTAGGAATGTAAAGTAAGTAGCTCCCATGTCTTATGACACATTTCTTGAGATTTAGAAAACTGAGGTTCATGCCTGTGTTGGAATGTTTTTAGTTGAGTGACATCAAAGCAGTGACTTGTCCTCATGGAGCCTATCTGCTAACCCACAAATATATAAAAATGAGATCGGAACATTTTAATAATCAGAGAAACAATAGTATGTGTCATCTTTCCAATATTCAGCAGAGTAGATACTCAATAGATGGGTAGGTTTATCGTTTTATACTGGTTTTAGACACAAAAACTATTTTTTGACAAGGAAAACCAATTAGGATTGAGTTCTTAACTTCCAACGTTATGAACCACTATTATGGCTTCACATTTCCCTACAGGGGTGGACATGCAGATTTGCCTAGGAGGGAGCGATTAACTATGCCATTGCATGTGGCAATGTGAGCTCTCCGTACTAAGCTGTTAAACTATATGCTTTATTGTCTCCTCCATGTGTGGCAAATAGAAACAGGCATATGAGCTGTCCGGTCTGACTCTGTCACATGACTTAG
Seq C2 exon
TTTTTCAGTTCTACCAGCTCTCCAATACCCAGCAGGACAGCATCACTGAAAAGGATGAAAGGCTGGGGAACATGTCCCGACAACTACAGTCCCTCCAGACCCAGAACAGAAAACTCACTGAAACTCTGCAGCAGGTAGCCGTAAAACTGTGTCGTGAACTTTACAACAAAAGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060460:ENSRNOT00000091602:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.176 A=NA C2=0.150
Domain overlap (PFAM):
C1:
PF043759=HemX=FE(23.6=100),PF041569=IncA=PU(29.4=73.5)
A:
NA
C2:
PF043759=HemX=FE(42.1=100),PF041569=IncA=FE(69.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACACCCTCTTCAGTTTGGC
R:
CTCCACTTTTGTTGTAAAGTTCACGA
Band lengths:
270-1462
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]