BtaINT0053826 @ 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
chr18:36241386-36243479:+
Coord C1 exon
chr18:36241386-36241529
Coord A exon
chr18:36241530-36243106
Coord C2 exon
chr18:36243107-36243479
Length
1577 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
CTATTGTCTTCCTTCTGTAGAAC
3' ss Score
10.38
Exon sequences
Seq C1 exon
GACTTTGACTTGAGCCAGTTACATAGGGGCCTGGATGCTCGGCCTGAAGTGACTCGCAATGACGTGGCACCAACCCTCATGAGTGTGCCCCAGTACCGACCCCGCCCTGCCAATCCTGATGAAATTGGAAACTTTATTGATGAA
Seq A exon
GTAAGTAAGCAAGCACAGTCAAAAGTCAAGGCACAACAAGCTTTTCTGTAAATTTGGAGAGAAGCAATTGCGTCAAAAGTGAGAAAAAGTCTTTAGGTTCTTTCCTTTACCATGTTTTCGTCTTGTATGATCCCTGAGCTACCTCCTCTTCCCCACCTATTTTTTTTTTTTTAATTTGTGCCTCATCTAAATTTCAGAACTAAAAGCACTTTGAATTAGTGTTTGGAAATTTGCAAAGTCTATACTGAAAAACTGAGACTTGTTTGAAAAGATTTAATAGAATTAGGAAGGAAAAAGAGATTCAAAGTAGATTCAGTTTGGTTTCACTAATGGGTCTCTTTCCCTGCATTGCACTGGGATGTAATATTAAATGTGTAATTTCAAGGCTACTTGAGGGCCACAAAAATAGCTTCCATTCTGTATATGTCAGAAATGCATTCAGCTATAAATACCAGAAGCTTAAATAGATACGATACCTTGTGCAAATAGAAGACTGAGGTAAGTAGTCTAGGCTGGAGCATCAGCTTTTTCCATCTTCCTGCTGCATGATCTAAGCATGTAGATCCTTGTTCTCATGCTTGTTGCCTCCTGATCACAAGATGGCTGCCACGCTTCCAGGCCTTGGGCCTGTTTTCCATTCAAGAAGTAGGAAGAGCGGAGCAGAGGACCAAAATCTTTCTAGCAAACTGTTAGGCAAGAAAGAAATTTATCCTTTAGGTTATTGGTCAGGACTTTTAATTAGCTTCAGGTAGGATGAGGAAGAAATGGTGGGATTAAGCAAAGAACCAGGGAAAATAATAGTCCAGTGGGATCTGTTTCCTTAAACTATGTTACCTGATTACTTACTCGGTCACTGGAATGATTTTCAGGGCTGGTCTGATGGTCCACTGGCCTTCAGTGAGACTTCATGGCTTTTAGCTTTCTAGGGGAGTTGTCATCACCAGGGACTCTAAAAACACAGCTGTGTTGGACAGGACCAAGCCAGATCCATTCTAGCACTGGGTCTTAGAGAAAACTGAGAACAGGAAGGGCCAGTTTAAACCATCCCTTTAGATACATCTGGATCAGGTCTTTTCCTCCATTTATGTTTATTTGTGCTTGTAGCTGTTTCTTAATTACAAAAGTAAAATGTTTGCTATTTTAAAAATATAAATTATGAAAATATATATAAAGAAAAGAATGTAAATCCTATGGACAGAGAATCTCATGAACAGAGGAACCCAGTGGGTCACAAAGAGTCGGACACAACTGAAGCGACTTAGCACGCACACAAGACTATCCTGGAATGACTGTTTTTAGTCTGTCCATTTGGATTGGCTGGTGCTCATCTCCCCTGCCTACATATCACTTACCACTTTTAACATTCTACTACAGACTTTTTCCTTTCATTAGAAATATATAATGACCATCTTCTGTTCCAGTCTGTATTAAGTTTACTTTGTTGGTGTTTCTGCAGGATGGTTGCATTGTTGTGTGTTGTGTGCATTTTGCTTTATTCACCAAGAGAAGGTATTTTGCTTAAGATGACAGGTGTGCAATTCCTCTCAATAAAAGATCCTATTGTCTTCCTTCTGTAG
Seq C2 exon
AACCTGAAGGCAGCTGATAGTGACCCCACTGCCCCACCCTATGACTCTCTGCTGGTGTTTGATTATGAAGGAAGTGGTTCCGAAGCTGCTACTCTGAGCTCCCTGAACTCCTCAGAGTCAGACCAAGACCAGGACTATGACTACCTGAATGAATGGGGCAATCGCTTCAAGAAGCTGGCGGACATGTATGGAGGCGGCGAGGATGACTAAGGGACTCAAGACTGATGGGAAGAGAGATGGGTCCCTACACTCGTGTGATGGAAAATGCGGGAAACATACTCCTGGTTGTTTGCCAGCTCCCTTCACTTGGGATACGTTTCTGGAGAAGAGACTGATCAGTGATAGCATAGTCCTGATTTCCACTTCATAGATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015991:ENSBTAT00000021272:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.739
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(31.8=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.9=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTTACATAGGGGCCTGGA
R:
AGTCCCTTAGTCATCCTCGCC
Band lengths:
346-1923
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development