RnoINT0043772 @ rn6
Intron Retention
Gene
ENSRNOG00000029945 | Cuzd1
Description
CUB and zona pellucida-like domains 1 [Source:RGD Symbol;Acc:619771]
Coordinates
chr1:201892729-201894775:-
Coord C1 exon
chr1:201894636-201894775
Coord A exon
chr1:201892880-201894635
Coord C2 exon
chr1:201892729-201892879
Length
1756 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CCAACTATGCCATCTACCAGGCA
3' ss Score
3.9
Exon sequences
Seq C1 exon
AGCCGACAAAACTCAGAAAACTATAAAAAGCCTGAGGGCTCTGAGGCACCCTGCCAAGATGGAGGTCACTGGAAGGCTGTTCATTTGGGCCATTTTAGCTGTCTCCTGTAGGGCACAGCTCAATTCTACAGCAGCTGAAG
Seq A exon
GTAAGAAAATTGAACCAGATTCTTTGACTCAAACAAAAAAGGCTTCCATGTCCGCCACTGCTCTTAACACAGAGAATAACTCACCCTTGTGCTCTCTGGACTTAATAGTCATCTCATTAAGGACCATATGGCCATGGTCACTGAAATTAAAAAGGGGGACATACAATTTTGTTTTTAATGCATATCTTAGGAAAATAATCCTAAAGCTATATAACTACATGACTAGATACTGGCCTAATTTTTTTAAAAGTAAGTTTCAGTTGCTGATTTTTTTTAAAAGGGCAAATCAATGGCAGAGAAATAATCTGTTAAGCTATAAAAGATTACATCTACAAGAAATGGGTCTCTGTTAAGAAGGAAAATGCCTAAGGTTTTAAAATATGATAGTGTTTATGTCTAGAACTACGCACAGAACTTCTTTAAAGTCAAAAAGAGAGGAGAAAAGGAAAAGACAGTTGAATTTGCAGAAGGTTTTAATAAAGATGTCCCTGGGTGGTTGGGACTGTGCCACCTCTTCTGTTCCCTTTGCTTTCTTTTCCTGATGAATACAGACCTAGTTATTGTTAGGTAAAGATAGACAGTTCCTTCATCAGTCATGGGTGAAAGAGAACTTATGAAGGCTTGTTTCTAAGTACACAGGGGTTTTATTGGTCTGTTTTGGAAAATGTGTCTGTTCTTGTCCTTGCTGGACAAAGACAGAGAGACAAAGACAGAGACAGACAGACAGACAGACAGACAGACAGACAGACAGGGAGGGGGGAGAGAGGGAGGGAGAGAGAAAGAGAGGAGAGGAGAGAAAAGAATCAGGGTCTTTCTACAAATCTTTGGCTGGCCTTTCTGTACAGGAGCCTCCTCCCTCAGCCTTCCAAATGCTGCACTCACTAATGTATGTCTCCACATCTTTCTTTCCCCATTTTTTATTGGGTTCCAGGTCTTTAATTTTTTTCTTTTTACATTTATTTATTGTGTGTGCTCAAGCACGCGTGTACTCACATATTACAGTACTCATGAAGGTCAAGGATCACTTCCTGTAGTTGGCTTTCTCCTCCTCCCGTGTGGGTTCTGTGGACTGGATATGTGTCGTCAGCCTTGGCGACGAATACCTTTACCCACTGAGCCATCTCGCTGGGCCCATCCTTTTTGTCCAATACTTTTTTTTTTTATTATTTAAAACATCTTTTTTTGAGTCAGAGTTTCCATGTGTAGCCCTGGTTGTCCTTTCTTTCTTTCTTTCTTTTTTTTTTTTTTCGGAGCTGGGGACTGAACCCAGGACCTTGTGCTTGCTAGGCAAGCGCTCTACCACTGAGCCAAATCCCCAACCCCGCTCTGGTTGTCCTGTAACTCCTCTGTAGACCAGGCTGGCCTGGAGCTCACAAAGATCTGCCTGCCTCTGCCTCCTGAGTGCTGGAATCAAAGGTGAGTGCCGCCACTGCCCAGCTGACCTATTTTGATCATATTCTTCCCTTCCTCCAAGTCCTCCCAGAGCCTCTTCTCCTCCCTATCCACCCCACTTTAAGTTCTTTCTCACAACAACCCTTAAGCCCAACACAACAACGAAGTCCTAAAAACCTAGAAAACAAAATCCATCAACACCCTAAAGGAGAGAAAGCTGTAATCAAATAAAAGCACACAAAAAAGTGTGGAGTCCGTTATATGTTGGTCAATTACTTCCCCTTCCTGTGGGAGGTTGAGTCCTAGTGCCTGCTGGGAGTCAGGGACTGCTCCTTTCCTCAGTGCCAACTATGCCATCTACCAG
Seq C2 exon
GCAGACCAAGATGCACGGCCAGTCTGGGAGGGGCCAATCTGGGAGAGACCCACAAGGCTCTGATCCTAAATCTCAATGCTGATGAGAACTGCACTTGGACCATAGAGAGACCTGAAAACAGGAGCATCAGAATCATCTTCTCCCACATCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029945:ENSRNOT00000050519:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043115=CUB=PU(29.0=52.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCGACAAAACTCAGAAAACT
R:
TGGATGTGGGAGAAGATGATTC
Band lengths:
291-2047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]