BtaINT0035457 @ 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
chr18:36130392-36134002:+
Coord C1 exon
chr18:36130392-36130616
Coord A exon
chr18:36130617-36133795
Coord C2 exon
chr18:36133796-36134002
Length
3179 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
TAATTATCTGTCTGCTCCAGGAG
3' ss Score
8.65
Exon sequences
Seq C1 exon
GGAGCCCTCCCACCACTGGCACAGGGACCCTCCTGCTAACACTGATGGACATCAATGACCACGGTCCGGTCCCCGAGCCCCGTCAGATCACCATCTGCAACCAAAGCCCTGTGCCCCAGGTGCTAAACATCACAGACAAGGACTTGTCCCCCCACACTGCCCCTTTCCAGGCCCAACTCACACATGACTCGGACGTCTATTGGACAGCAGAAGTCAACGAGAAAG
Seq A exon
GTAACTGAGTGGTGGTGGCAAATGGGTCCTCTCTCCCCTACCAAGATCCAGCATCTACCTTCCTGCTCCATCTTGTGGGTCACCGAGTTACCGGTCTCCTCAAGAATGTCAGTCAGGGGAATTCCCTGGCAGTCCAGTGGTTGGGACACCTGGCTTCCACTGCAGGGAGCACAGGTTTGATGCCTGGTCAAGGAACAAGATCCTGCAAGCTGCACAGCCAATAACACACAAAGACGATGTCAGTCAAATGCTGCTTATTAACTTAGTCTAAACCTTTGGGAATCCACAGGAATCCTTAAAGACCATTCTAGCCCAACCACTTTCCTATACAGTTGGAAGCACTGAGGCCCAGAGAGAGATGGGACATGCCTTTCTCACTATGACATAATGAGAGAGTCGGGAACCCAGCACAGTAATAACTAACATGCCTGAGCATGCTTGCTATGTGCTATGTGCACTTCAGACACTTCACACAGATTCGGCTACTGAATCCTCACAATAACCCTGTAAAGCAGGTACTGTTAATCATACATATACATGTATGTGCACCCGTTTGACAGATAGGGAAACCAGGGCTTATAGAAACTTAAATATCCTGTCAGGGGCATTATGGATAGAAAATAATGGCCCCATGATTGGGATGCAGGAAGTCTGCTCTACCAGGATCCTCTGCTGCCTACCATTTATCCACCCCTGGACATTTGCAAGATGCTTTTTATACTTATTTTAAATTTCTACCATCCTCTGTGATCAGTATTTTTATCCCTATTTACAGATGAGAATCAGGCTCAGAAAGGTTAAATGGCATGTCCAAAGGCACAGTGTGGGTAAACAGTGGAAAAGAAGTAGAAGACAAGGTCCCTGGCCCTCATGCCCCTGCTCCCAACCACCTCCCTGTCCTTTCTCTTTCCCACCCCATAACGCTCCTCAGCCTTCAGTGGTTTTTCAGTTGTTACAGGACTGAAGAGGAGACTTACTGGCATCAAATGGGCAAGGACTCAGGTGCGTAAAAACAGTGCATCCATGCCCAAGTGCCAATAAGGCCCCTGGAGAAGCTCACCCTGGTTTAAAATGCCTCCCTCTTCCTCTTGGTGCTAGGTCCCCCAAGAGGGGAATGGGGAACCAGTACATTCAGGTTCTTCCCTGAAGTAACCAAATGCCTGGTGTCTACTGCTGCTGCTGAGCCTGTCCAGAAAGGACTGAGGAGACCTGCCTCAGACACACACATTGTCCCGTTTTTATGATTCCTCTGATTTGGGGGTATATACTCAGCACCTTTCCTCGAGGAAGCCCAAGTTGGTCTCCTATTACCTCCCTGTGGCCTGAAAGCCATTTTCCCCTCCCTGACTGGTTTACGGAGCATAGCCTCTGAAGTCAGAACACCTTGGTTCAAGATCCAGCCTCTCCATTCACCAGCTTGTGGGCAAGTTACTGAACCTTACTGTTGAGCAGTTTTCCCCACCTGGAGGATGGTGCCAGTAATTGTACCTCTGTACAGTCACTGTGAAGACTGAGTACACGACAGGCACCTACCTCTTCTGGTGCATCAGTGCTCAGTCGATGCCAGTGGCCGTCTTCACCAACAGGCACAATCTGGCTCTGCCAAGAGTGAGCGTTACCTCAAAGCCCAGTGGTACCAACGCCTGACACTACCATTGGTTCTTGGTTTTGACTTAGTCGTTTTATCTGTCTGTGTTCTATTGTGAGAGGAGTTAATCCCAACTCTACACCCATGTGAACTGGGCTCGTTACTTGACCTCCCTAAGCTTCAGTGTCTGTATTTGTAAAATGAGGGGTAACAGAACCTGTCTCTTAAAGTTGAGGTGAAGATCAGAGTCGGGCTTGGCATGTAATAAGTGTCAGTTGAGTCCCCACTGCCACCACCAGCACCATCATCAGCTGAGAAGTCAGCTCTCCAGCCTGGGAGCAGGAAGGCAGGAGGGATGTTCTGGTGAAATGCCCCACGTTGGCCTCTCCACTCGGTGGACCAGACATCCAGCGTGCAGAACTCTGTCTGTCTGCCACTGCTGAGTGGGAACAGGGTGAATTCTCCCTCTGGCCTTTCAGCTAAGAGGGGCCCAGGGAGTGTGCAGAGCCTGTGAACTGAAAGTGGCTTGAGGTCAGTGCTGAAATAGGCCAGCAAGCCTGAGGGCAGGTGGGCTGGAAACGCGGGATTGTTTTTGAATGTCCCAATGATGCGTGGGGTTGGGGGGGCACTGTTAGCATTTAGTGGTGAGGACTTGAGTGCTCAGGAAAGTTCCTCGTGATGAAGAATAGTTCCACCCAAGCTAATAGCACCCACCTTGAGAAACTTGGGTCTAAACCGAAGGCCTTTCTGCAGAGAGGCCTCTGACCTTATATTTCTCACCCACAAACATAGCCCCCATCCCCACTCCATGATGGCCAAGCAGCCTCCCCAGAGTGGCTCCCGTCGTGCAGGCTGCTCCAAAGCTTGGCTTCGGCTCTGTGGCTGCCTGCTGCCTGCCCCAGGCCTTCAAAGGCCAGTTAGCACGGTGCCCAGCACAGCCTCACTGCCAGCACCTCTGAGCTTGTGTGCAGTCACTAATGCTCTGATCTGCTCCTGGCATCAGTTACATCGCCAGGTAATATGCATTTGGATTTCTTAATAACTGATGCTCACTCAGAAATATCCAAGTTTCAGATATATTGAAATTCTATCATAGAGTTAAGGTATAAACATTATATATACAATTGAAAGAGCAAAATGCTGCCATAACAAGTGGTAGTAAACTTTCAGGTAGAGAAACAGGTGGCCAGTTAATATAAATATTAAAAGATTGTGCTAGCTGTCTCTTAGGAAGAACTTTGTTTCTTTGCTTGTTTGTTTTGAAGCAAAGAACAATCTGGCAGCTAATAATGCTCAGAAATTATTGGCCCTGCATGCCATGAATTTTTTAAAATGTCATATTTAGAAATACTGTGATTATTGATTTTCTTAAATAGAATGATGACTTTATTCTTCTATCCAAATAATCCTTCCCTCAGTGGAGGATTTGGCTTGGACCAAGTATCCGTTTGTAACACTTGGCGTAAGTTTGCTTTGACGACATTGCTCCCTGTGGCCCAGATGCAGTCTGCCTCCTCAACTCTCCATCATGGTGTGCTTGGCTCCCACCATTTGTGGCCTTCCGAGGTGAATAATTATCTGTCTGCTCCAG
Seq C2 exon
GAGACGCAGTAGCCTTGTCCCTGAAGAAGTTCCTAAAGCAAGGCGAATACGATGTACACCTTTCCCTGTCCGACCACGGCAACAAGGAACAGCTGACAGTGATCAGAGCCACCGTGTGTGACTGCCACGGCAACATGGTGACCTGCCGGGACCCCTGGACGTGGGGTTTCCTCCTCCCCATCCTGGGTGCTGCCCTGGCTCTGCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000033248:ENSBTAT00000045591:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.329 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(54.5=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.3=55.7)
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:
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