RnoINT0043774 @ rn6
Intron Retention
Gene
ENSRNOG00000029945 | Cuzd1
Description
CUB and zona pellucida-like domains 1 [Source:RGD Symbol;Acc:619771]
Coordinates
chr1:201889021-201890589:-
Coord C1 exon
chr1:201890375-201890589
Coord A exon
chr1:201889172-201890374
Coord C2 exon
chr1:201889021-201889171
Length
1203 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
CTGTCTTTGTGTCTCTCCAGCTA
3' ss Score
10.87
Exon sequences
Seq C1 exon
GTTGGATCCAGACAGTCGGTGTGAAAATGAAAGCATTAAGGTGTTTGATGGACGCTCCACCAGTGGGCCTCTGCTAGGGGAGGCCTGCAGCAAAAATGACTTCGTGCCTGTGTTTGAGTCATCGGCCAATTCACTGACGTTTCAGATAGTCACTGACTGGACAAGGGTTCAAAGGAGTGTCTTTATCTTCTACTATTTCTTTTCCTCTGGTACCA
Seq A exon
GTAAGTTGTCCATGACCCTTTCCCCTGCCCTCTGTGAGCACTGGTTACACCAGCTCCTGATGGGGACATGGTGTTCTTGAGTCTGTTCCCTCATAGCAATAGCTGGTGAAAAGGCTATTCTCCAGGGCCGTGCACAGAAGAGTCACGGGTTCAGTCACCTTTGAAATCTGATTCTTTGGTTCTGGGGAAGCTCCTGATGCTCTTCCTCCTCTAACCAGTCCCAAAGCTCACCACACAGCCACAGGTTGACAAGCACTGTGTCTGAGCCCAAAGGACTCTGTTTAGCCTGTTTTGTAACCTGCTGCTTTCATTAGATGTGGGTTGAGGCTCTTGAGCTTTTGTGCTTATCAAGTTCTGGGAGGGGGGTGATTCTGACAACCAAGCAAATGTGGGTGAGACTGAGCCAGTTTGGGGGCAGTCAGGTGCTACACAATTCTATGTAGTTGGCCCCCAATCCCAATTCCCCTCAGCTAGAATGCCATGGACTTGAGCCAGCAGGTTCATAAGGAGAACTTCACTCTGGTTTTCTAGAAGAGCTGATCTTAACACAGATATCTTGTGCTACAGAATCAACAAGGTAGAGACATCAAGCTCTTCCAGAGCTGGACCCAGGCTACCTCCTCACACCTGACATGGAGACCCTACTTAACATGGGTCCTGTGTGCCAGCCAACCTAAACTATTTTATACCCATAGGTGTCTTCAGTTTGCTTCTCTGTTTTCTCTGTCATGTTGCCCTCTACAGTATGTACAATAGCAGGGAAGGATAGAGAAAGGTTGCATCTGAGGTGAACTTTGAATATTAGCCTGAGGAGAGAGTAGTGGAGGACTCTATATTGAAGTCCTAGCAGACATGTTAAGAAAGGGCAGTGTAGAACAACAGCTCCTTTGGTGATAGCCAGCGATCTTGGACAGTGATGATAGGTAAGGATCCTTTAGCACCAGCCCTAAGAGCGTGGCTACTTTCTGCAGCTCGGTCCCGGTGGTGGAGGGCCTCTCTAGCCAGTTCAGTCACTTTATTATGATTTGACAGCGGGGCAGAGATGTGCTCTCAGGTGTCCCAAGGGCAAAAGGTCTGATGCTAAGAGAAGAAGAAGACCTCCAATGTGACCCACAGAGAAGACAGGGGTGGTGTGACACTCAGGGAGGACATGTTAAACTCCATATATCACAGAAAAATCCAACTGTCTTTGTGTCTCTCCAG
Seq C2 exon
CTATTCCAAACTGCGGTGGTTACCTGCAAACATTGGAAGGATCCTTCAGCAGCCCCAATTATCCAAGGCCACACCCTGAGCTGGCATACTGTGTGTGGCACATACAAGTGGAGAAAGGCTATAAGATAAACTTGAATTTTACAGAGCTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029945:ENSRNOT00000050519:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(69.9=89.0)
A:
NA
C2:
PF0043115=CUB=PU(42.2=90.2)
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:
GTTGGATCCAGACAGTCGGTG
R:
ATCTTATAGCCTTTCTCCACTTGT
Band lengths:
342-1545
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]