BtaINT0035453 @ bosTau6
Intron Retention
Gene
ENSBTAG00000033248 | CDH3
Description
Bos taurus cadherin 3, type 1, P-cadherin (placental) (CDH3), mRNA. [Source:RefSeq mRNA;Acc:NM_001244605]
Coordinates
chr18:36095734-36096125:+
Coord C1 exon
chr18:36095734-36095772
Coord A exon
chr18:36095773-36096004
Coord C2 exon
chr18:36096005-36096125
Length
232 bp
Sequences
Splice sites
5' ss Seq
CTGCGCTTC
5' ss Score
-22.5
3' ss Seq
TCTTTCCCTCCTTCCCTCAGGCA
3' ss Score
11.72
Exon sequences
Seq C1 exon
ATGGGGCTCCGTGGTGGGCCTCTCGCGTCCCTCCTCCTG
Seq A exon
CGCTTCTTTCTCCTACTCCAGGTACTCCATTGCCTTGCCCTGACCCCGGCCGGAACGCTCCTCAGAGGGCTGGCGGGAGGGGTCCGCACGCGGCGGTGGCGTCCGGGAGAGCGCGGGGCTGGGCTCCGTGGGGCCAGGGTTGTCCGGGACAGCCTGTGAGGACTCCCCGGGATGGGTTTGCAGGGCCGGGCACGCCTATGACCCAGCCTCCCTCTTTCCCTCCTTCCCTCAG
Seq C2 exon
GCACAGGTTTACTGGCTGCCGCGCGCGGCCTCGGAACCGTGCCGGGCAGGCTTCGGGGAAGCTGAAGTGACCTTGGAGGCGCGAGGCGCGGAGCTGGAGCCGGGCCAGGCGCTGGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000033248:ENSBTAT00000045591:1
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:
PF087586=Cadherin_pro=PU(42.4=68.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
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]
SPECIAL DATASETS
- Pre-implantation embryo development