BtaINT0084370 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011966 | LAMC1
Description
Bos taurus laminin, gamma 1 (formerly LAMB2) (LAMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206817]
Coordinates
chr16:65632327-65632934:+
Coord C1 exon
chr16:65632327-65632463
Coord A exon
chr16:65632464-65632811
Coord C2 exon
chr16:65632812-65632934
Length
348 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAAG
5' ss Score
5.75
3' ss Seq
TTTTCATCCTCCGCTTGTAGATG
3' ss Score
10.08
Exon sequences
Seq C1 exon
ATGCAAACCTGGATTTTTTAATCTGGAATCATCTAACCCTAGAGGGTGCACCCCCTGCTTCTGCTTTGGGCATTCTTCCGTGTGCACAAATGCCGTTGGCTACAGCGTTTATTCTATAACCTCCACCTTTGAGACTG
Seq A exon
GTAAAGTAGACCTTTCCTTTAGTCCCCTAGAACGTGGAGCCTAGGCTTACAGTATTAAAAAAGTCAGTAACTCTTAAGATTTTTTGAGACTATCAACACTTTTTCTTTTAATGTATGTGATTTTTGTTTGGCTTTTAATTTAATGAAAACATATGCAGATGGTTTTAGAATTTACCTGGGAGTATAAATGTTATATAAAATAAAAATACTGCTTCAGAGGTATAGCATATATAGGTACTGTTACAGCCTCCATTTACTCAAAAACTTTGATTGATGACTTTCTGTACATTTTGTGGAATATAGAGGACCTGAATTCAGGATGTTTGTGTTTTCATCCTCCGCTTGTAG
Seq C2 exon
ATGAGGATGGGTGGCGTGCAGAACAAAGGGATGGCTCTGAAGCATCATTTGAGTGGTCCTCTGAGAGGCAGGATATTGCCGTCATCTCAGACAGCTACTTTCCTCGGTACTTCATTGCCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011966:ENSBTAT00000015881:8
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=0.119
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(33.3=34.0)
A:
NA
C2:
PF0005213=Laminin_B=PU(3.8=11.9)
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:
TCTGGAATCATCTAACCCTAGAGG
R:
CAGGGGCAATGAAGTACCGAG
Band lengths:
239-587
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development