RnoINT0032269 @ rn6
Intron Retention
Gene
ENSRNOG00000020884 | Cd6
Description
Cd6 molecule [Source:RGD Symbol;Acc:2312]
Coordinates
chr1:226851934-226853534:-
Coord C1 exon
chr1:226853439-226853534
Coord A exon
chr1:226852051-226853438
Coord C2 exon
chr1:226851934-226852050
Length
1388 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ACCCTCTGTTCTCTCCCCAGCTC
3' ss Score
11.55
Exon sequences
Seq C1 exon
CCCTCCCTACTTCAGTGAACCACCAGCAACTGTCCACTGCCAATCCAGCAGGGATCAACAACTACCATCCTGTCCCTATCACCATTGCCAAAGAAG
Seq A exon
GTAGGAGGTCACTCACGGGGAAGGCAGGGGGAGAACAGGGAGGGTAGACTCTAGAAGGTCACCACTGCTGAGGCTAAAATGACAGCAAGAAAGGGGAGCCCAGGCCAGACTGTGACAGACTGTGTTGCCTTGAGCAGTTCTCAGCCTTAGGCTTAGCACACAAGTGACCTTCTGCTCAGTTTTGTCCACCTCTGGGCTCTTGAGTTCTGGGCAAATGCAAGCCGAGTGTTCGAGATGTTGGTTCTCAGAGGAAAGGTTGGCTTTGCTCACTGGCTAGTAGATTTGTTATGTCACTTCTCAAGATGCTTCCCAGCCAGATGCCCAACAGAGCCTTCCCAGAACAAGGGCTGGGGTGTGGCTATGTTGGTAGAGTACTTAATACATACAGGCCCTGGGGTCCAATGTCCAACACCACGTAACCCAGACATGACGTGGCACTCCTGTAATGCCAGAACTTTGGAGGCAGAGTTCAGGGTTATCTTGAGTTTGAGGCTAATATGAACTACATGAGACCCTATTTTAAAAAAAAACTTTTAATTTTTTCATTTTCTCTGAATAAAAGAATTAGGGCTGGAGAGATAGCTCAGTTGGTTAAAGTGCTAGCCTTGCAAACATGAGGAGCTGAATTCAATCCCCAGTATCCATGCAAAAGTTGGGCATGGTAGCACGAAGCTATAATCCTAGTGCAGGAGAGGCTGAGATGAACAGATGGTTGTGGCTCCTGGCCAGGCAGTCCAGCCTATTCAGCAAGCTCTAAGTCCCAGTAAGAGAACCTGTGGAAATGTGGTGCAGGGCATGGTGACCATAGCACATGGCTTTAATCCTAGGGTGCCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAAAGGCAGAGGCAGGCAGATCTCTATGCATTCAAGACCAATTCTATTGGCATAGAAAGGTCCAGCCAGCCAGGGATACACAGTGAGGCCCTTATCTAAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACGGGGGTTGGGGGGACTCACTCTTTAGGATACATAATTTGCCTCCGAAGAATTTGAGTTCAATCTCATTGCATTTTTTGAAACAAAATTGGTCATTTGCTACTCTGCTCCCTGTCCCTGCTACTGGCTCTCTGCCCTTCCCCTTAAGCCTTCTGCCCATCTCTGGGTTGTGCTCTGTCTCCCAACCCTCTGTTCTCTCCCCAG
Seq C2 exon
CTCCTATGTTGTTCATCAAGCCCCGGGTCCCCGAGGACTCGGACTCCAGTTCTGAATCCGACTATGAGCATTATGACTTCAGCTCCCAGCCGCCTGTGGCCCTGACCACCTTCTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020884:ENSRNOT00000028347:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF054546=DAG1=FE(20.8=100),PF151021=TMEM154=PD(16.0=48.5)
A:
NA
C2:
PF054546=DAG1=PD(15.6=60.0)
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:
CCCTCCCTACTTCAGTGAACCA
R:
GTAGAAGGTGGTCAGGGCCA
Band lengths:
212-1600
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]