BtaINT0035460 @ 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
chr18:36137329-36140923:+
Coord C1 exon
chr18:36137329-36137475
Coord A exon
chr18:36137476-36140085
Coord C2 exon
chr18:36140086-36140923
Length
2610 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CCCTGCTTTCCATCCCCCAGAAC
3' ss Score
10.04
Exon sequences
Seq C1 exon
GACTATGACATCACCCAGCTCCACCGGGGTCTGGAGGCCCGGCCTGAGGTGGTTCTCCGCAACGATGTGGCACCATCCTTCATCCCCACACCCATGTACCGTCCTCGGCCAGCCAACCCAGATGAAATCGGCAACTTCATCATTGAG
Seq A exon
GTGAGGCATGGGGGCCCAGCCTAGGGCAGTCCTTCGTTCAAGCACCAGCAGCTTGAGAGAAAGAGCACAGGCTTGGAGTCTTGGCTGTGGGTTCAAATCCTGGGTCTGTCACCAACAAGCTAGCTGTGTGACCTCTGGCATATATAGCAACTTCTGGGCCTCCTGTTTCCTCCTCCATTAAACCCAAAGTTTCGAAGTGGTTAAAGAATAGGTCAGGAATTCTTTCTTTTCTTTTTATTTGTTGATGTTTATCATCTTCCCTGGTGGCTCACATGGTAAAGAATCTGCCTGCATTGCTAGAGACCTGAGTTCGATTCCTGGAGTGGGAAGATCAACCCACTCCAGTATTCTTGCCTGGAGGATTCCATGAACAGAGGAACCTAGCGGGCTACAGTCCATGAAGTCACAAAGAGTCAGACATGACTGAGTGACTAACACTTTCACTTTCATTTATCATTGAACAAAAGTAAGAGAGGACTGGGTCTGGCACAGATGAACAATTTGATCAATAAAAACCAATGAGGAAGAGCAGGCTCTGTTGCAGTCTAGATGAATTCAGAGTCAAGGCTCTTGACTTTTCCAGGTGATCTCTGGTTTGACAGGATTTTTGATTAGGAATTATTTCTTTATTCAACACATATAGTGGTTGTTAGGAGAAAACTCGGAGCCGGACTCCCTGGGTTTGCATTTGTAAAGATCTCAGGTGATTCCAGCGTGGAGCAAAGTTGGGGGCCTCTGGGATAGGTTGGTTTAAGGACTGGATGAGTAAGGACCGAGCAGTGCTGGCTCAGGAAATCTCTTGGGGAACTTCAAACACTGAAGCCTCTGACACCCCCCAACCCCACCCACCCCACCCCCTGGACTGTGATTTAATTGATCTGCATGTGGGCTAGACTTCAGAATATTTTTTTTAAAGATTCCCAGGTAATTCCCCTTGGCTATCTATTTTACATATGGTAATGTAAGTTTCCATGTTACTCTCTCCAGAAACTCAAACCGGGGCTCTGTATCAACCTAGAGGGGTGGGATGGGATAGGGAGGGAGATGGGAGGGAGGGGATATATGTATACCTATGGCTGATTCATGTTGAGCTTTGACAGAAAACAACAAAATTCTGTAAAGCAATTATCCTTCAATTAAAAAGTAAATTAATAAAAAAAAGATTCCCAGGTAATTTAAGTTTGGGAACCACTGGCCTGGCACCTATCCTGTATTAATTAGGTAATGACAGCTCTTGTTGCTAAGTGTCACCCATATTCTCAATTCTGGGCACATACTTGATTTATCTAAGGAATTTTTTAAAGTATCAGTGACTCGAACCCAGATATTCTTTTTTTTTTTTTTTTAGGCTCTGATTTTTTGGGTTTTTTTTTTTTGGCCATGCTCCACAGCATGCAGGATCTTAGTTCCCCAACCAGGGATGGAACCTGTGCACCCTGAAGTGGAATCGCAGAGTCCTAGCCACTGGATCACCAGGGAATTCATAAGCTCTGATGTTTCTTTAGTTCCCCAAGAAATAAAAGATACAGGATATATATATATATATGAAATAAAATATACATAGGAGATAATGATGTGAGGCTAGCATAGGCTGGTACCATGAAAGTAGTCAGTAAAAGGTTTTTAATAAGAGGGAGGGAAGGAGGAGGGAACAGAAGAGGAAGGAGGGAAGGACGGATGGATTTGGGAGGTTGGAGAAAGCAGCAGTAGGCACAGGGCTCAGTGGGTGGTCAGGATACCTTACTTTGGCCTGAACTCGGCTTACCTTTCTTGCTTTCTCGAACTAGCGAGACTCCGTTCTTTAGCCTTAAGCACATTTGAGAATCCTGTACAGAAACAAAGGCGTCTGGGGAATGTTGCTCAGGGCATCTTTGCCTTGGAGCCAAAGGCCAGGAGATCTTCTGACAGTTTTCAGAATATTTGTGTCGGATAGTTTGCAAATAACTGTCTGGTTTAATGCCTCGCTGTGTCAGCTCTGCAAAGGAGGAATTCTGTTATGGTCCCCTGTAACTCTAATATGCACTTTTATATTTATATACATTCATTTCTCCCTCTGAAACTATATGAAGTCTCCCCATTTTTGAGATGGAGGGCTTCCAAGGTGGCACGGCAGGAGACATAAAGAGACGTGAGTTCGATCCCTGAGTCAGGGAAGATCCCCTGGAGGAGGGCATGGCACTCCACTCCAGTATTCTTGCCTGGAGAATCCCATAGACAGAGAAGCCTGGCAGCCTGTAGTCCATGGGGTTGCAAAGAGTCAGACACAACTGAAGCGACTTAGCATGCATTTTTGAGATGAGGGAAACAAAGGCATGGAGACTTTAAGAGGCTTGCCCAGGTCTACACACTCAGAAGTCTGTGTGAAGTCTGACTTCAGAGTCCCCACCCTGATCCGCTGGCCTGTGGCGCTGAGCACTCGCTTTCAGCTGGGCCCTGAGCTAAGGATTTATGTGCATTTCGTGTTCAACCTTCAAAACCTTAAGGGAGGGGAGACAGGGCTTCACAGATGAGGAAACACAGGCTCAGCCAGATGAGTTCACTTTTCTGAGCTCTCGCAGCTGCCCAGTGTCTGGTCCCACAGTGCCTAACACCCTGCTTTCCATCCCCCAG
Seq C2 exon
AACCTGAAGGCAGCCAACACAGACCCCACGGCCCCGCCCTACGACTCCCTGTTGGTGTTCGACTATGAGGGCAGTGGCTCCGATGCCGCCTCTCTGAGCTCGCTCACCTCCTCAACCTCTGACCAGGACCAAGACTACAACTATCTGAATGAGTGGGGCAGCCGCTTCAAGAAGCTGGCGGACATGTACGGCGGGGGCCAGGACGACTAGGACTCCCTAAACGCCGGGCTGCAGCAGCGTCTCCAAGGGGTCACTATCCCCACGTTGGCCAAGGACTTTGCAGCTTGTTGAGAATTGGCCTTAGCAACTTGGAGGGAAGAGGCCTCGAAACTGACCTCAAAGGGGCAGGTCTCTATGCCTTTCAGAACGGAGGAACGTGGGCAGTTTGATTTCAACAGTGAGCACCTCTTAGCCTAAGCCAGGGCTGCTCAATTTCTGGGAGTCTCCTCGCTACCATAAAATGCTCAGCGCTGGGTCCTGGGTTTTGACTGACTCTGACTTTCCCATGATGGCTTTTGCTCTGGAATGGACCCTTCTCCTTAGTAACAGGCCTCTTACCACAATCTTCGTTTTTTTTTTTTTAATGCTGTTTTCAAAAAGTGAGAGGCAGGTCCTCAACCACCCCCTGGAGCGCTCCAGAAGCCCAGGCGTGCCCTCATGCATTTCTCTGTGGTCTCTTGGCCCCCAGACCTCCTGTTTGATTGGATAACTGCATTTTTATACTGAGCACGTCTAAGTGGTCCTTTATTTTTTATTTTCCCTATCGAGTGCTGTAGATGAAGAGTGATGACAATCCTGTAAATGTACTAGAACTTTTTTATTAAAGGAACTTTTTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000033248:ENSBTAT00000045591:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.377
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(32.0=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
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