BtaINT0087705 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012844 | LRSAM1
Description
Bos taurus leucine rich repeat and sterile alpha motif containing 1 (LRSAM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001075296]
Coordinates
chr11:98228126-98229896:+
Coord C1 exon
chr11:98228126-98228262
Coord A exon
chr11:98228263-98229180
Coord C2 exon
chr11:98229181-98229896
Length
918 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CGCTCTCCCCCAACCCCCAGGCC
3' ss Score
10.12
Exon sequences
Seq C1 exon
AGCTGCTGAAGCCACCTGAGGGCGGGGTCCTGCCCACAGCCCCCGAGGAGCTGCCTGAGGCAGTGAGACCCTCAGCTCCCCCCGCAGAGCTGCTGGAGGTGCAGACCTCAGAGTGTGTGGTGTGCCTGGAACGGGAG
Seq A exon
GTAAGTCTAGGGGTGATGGGCCCGACCTCCGGGGCCACCATCCCCGCCCCCTACCCGCCTGCCCAGCACCTGCCGCCCTCTCAGGCATGGGTGATTCATTCTGCCGAGAGTTTAGAAATATGTTGTGTTCATTAGAAATTTTCGAAAATACAGGGAATTAAAATGACCCATGATCCCAGGACCCAAAACATGAGCAACGCTGACAGCATTTGCTGGGCCTTTTTTTTGTTTGTTTTTTACAGAAGAGTTTTTTAAATTCATGCAGGGTAATTTCCCAAGTCATTGAATATCAACAAAATTTTCTCTGGAGAGGTTTTTTTTTCAAAACTCTTAGTTTTAACAACAAATTTAACAGCCGTTATAAAAAATTACCGTAGTATATAAAATAAACCCCTGTTCTCTCCACCACATGATCCTACTTAGAAAAGGCCACATGTTAACAGTTTGGTTACCCCGTGGTCTTTGCTGGCCCCGGGGAATGCCATGATATGGGGGTGGGGGAGGACTTGGTTATGAATTTAACCAAACCTCTCCTGCTCTGGGCCCCAGAAATGGCTTCCTGTCTCTCCTAAAAAGTGGAAATGCTGAGGCAAAGCATGGAAACATCCACGGCTTGTGATCCGTAATGTTGGGGTCATTTTGAGGCAAAGTGCATAAAAATCCCTAAATTGGGAGCAACCTGCATATCCTGTAACAGCAGGGCTGGTGAGACAGGCCATGGACCACCCTCCCCCCAACCCCGAACGGCTGCTACAGAGGGCCGGGGCATGGACGTGTCCAGGGAGGGTGGTGGCATCCTGTGGTGGACGGGGAATGGAGTCTGACGACTCTGTGGTCACATCTTCAGGGGGAAGGACAAGGGGCCGGGGCACCAGCCGGGGTGGGGCCCTGACGTCCCCGCTCTCCCCCAACCCCCAG
Seq C2 exon
GCCCAGATGATCTTCCTCAACTGCGGCCACGTCTGCTGCTGCCAGCCGTGCTCCCAGCCCCTGCGCACCTGCCCACTGTGCCGCCAGGACATCACCCAGCGCCTCCGCATCTATCACAGCAGCTGAGCGCCAGCCTCTGCCGCCCTCGGGCCCAGGGCTGTGCTCCCTCCTGTTCCCCACGGGCTGGTCCGGCCCTGCACCACACCGTGCCCCCGTCCTGGGCCAGGCTGAGACAGGAGCGTTCCTGCCCAAGTACTGAGCGGTTTAAATCCTGTAGAGGGGGTGGGGGGACCCCTCGCGGCAGGACCACAGGGTCTGGGGTGGGAGCAGCGGCAGCCACACCTCCGTCTGAGCCAGCACCGAGGGTTCCAGCTGCCTACGGTGGTCACAGCCCCTCCTGGAGCCTTGGTGTCTTCCTCAGGGGAACCCGGGCAGTGCCGTCCCACTCAGCAGGGGTGGTGGGAGCCCTGGCCCAGGGCAGGGGCGGCCACCGCGGCCTGTCCTGGGATCGACAGGCCAGAAGGTGTTCAGCGCGGGCCTGGTGCCCCAAGCAATGTCAGCCCCTCCTGGCCTCCCTCCCTGCTGCCCCCTCCCCCGCTGAGCTCTGGGCCCCTCTGCTCCGCAGACCTGCACCTCCTCTCCCCATGCAGCTCAGGAGAAGACCCTGAGCTTCAAAGACCTGAAGCAGGAACGTCAATAAACCCATCTCCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012844:ENSBTAT00000017067:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.522 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139201=zf-C3HC4_3=PU(23.9=23.9)
A:
NA
C2:
PF139201=zf-C3HC4_3=PD(71.7=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGGCAGTGAGACCCTCAG
R:
CTCAGTACTTGGGCAGGAACG
Band lengths:
343-1261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development