BtaINT0053824 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015991 | E-CADHERIN
Description
Bos taurus cadherin 1, type 1, E-cadherin (epithelial) (CDH1), mRNA. [Source:RefSeq mRNA;Acc:NM_001002763]
Coordinates
chr18:36239670-36240685:+
Coord C1 exon
chr18:36239670-36239900
Coord A exon
chr18:36239901-36240554
Coord C2 exon
chr18:36240555-36240685
Length
654 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
CTCTCTCTTCCCTACTCCAGTCC
3' ss Score
8.81
Exon sequences
Seq C1 exon
AACGTGAGTCTCTGATTTTGAAGCCAAAGAAAACCTTAGAGCTGGGTGACCACAAAATCAATCTCAAGCTCATAGACAACCAGAACAAAGACCAGGTGACCACACTTGATGTGCACGTGTGTGACTGTGATGGGATCGTCAGCAACTGCAGGAAGGCCACGGCCTTTGCTGAAGCAGGATTGCAAGTTCCCGCCATCCTGGGGATCCTCGGAGGCATCCTTGCTTTTCTGA
Seq A exon
GTAAGTACTGCTGGCGAGTGTTCCAGCCTTTTGCTTCTACAATGTTAACTGTATATAACCCAAGATCAGATGAAAACCTTGAAAATTAATTAATAGATTTTAAAGCTTATCTTAAGATAAAGCATATGCCAAGTAATTTTTTTGCTGTCATTTATTTTTAATTTTTAAATTTTTTAATGTTTTTTCATTGTGTGCTATGTGATTTTATAGACTGTGCCCCACCCCAATAACTGAATAATAATAATATGTATGTATCAGAAACCTTGAGGCTGATACAGCCCTTGTCGCAAACCATCAACAGCTCTAACTCAGAATCAAAGCCACAGTCTCCCCAGAGGTCCACAAGAGGTCCCTCCGCTGACCTGGCCTTTCCTTAATCACACCAATTTGCTCCTGCTGCAAGGCCTTTACTTGGACCATTTCTGCTCCCGGAGTACTTTGCTCCAGATTTTGAGAAATGGCTGATGGGTTTAAGGTCCAATTAAAGACCACACTTGAGGTCACGTGTACTTGTCTACTGTGTTGTGCTGCATATATTAACTTGAGGGCTGTGAAGACATGTAAGTTGCCTAACAGCCGTCTATCCAGTCTGTGCTGGCTGCTGCTTACATCCTTGCTGATTTGTGGCTCTCATCTCTCTCTTCCCTACTCCAG
Seq C2 exon
TCCTTATTTTGCTGCTTCTGCTACTTGTTCGGAGGAGAAGGGTGGTCAAAGAGCCCTTACTGCCCCCAGAAGATGACACCCGGGACAATGTGTATTACTATGATGAAGAAGGAGGTGGAGAAGAAGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015991:ENSBTAT00000021272:11
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=0.364
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(44.9=51.3)
A:
NA
C2:
PF0104912=Cadherin_C=PU(22.3=75.0)
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:
CGTGAGTCTCTGATTTTGAAGCC
R:
TCTCCACCTCCTTCTTCATCA
Band lengths:
350-1004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development