BtaINT0084364 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011966 | LAMC1
Description
Bos taurus laminin, gamma 1 (formerly LAMB2) (LAMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206817]
Coordinates
chr16:65660303-65662819:+
Coord C1 exon
chr16:65660303-65660402
Coord A exon
chr16:65660403-65662353
Coord C2 exon
chr16:65662354-65662819
Length
1951 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GTCCTCTTCTGACTCTGTAGGGC
3' ss Score
8.81
Exon sequences
Seq C1 exon
GCTTCACAGGCAGCTCAGGAAGCCGAGATCAATGCCAGAAAAGCCAAAAACTCTGTTACCAACCTTCTCAACCTTATTAATGACCTCCTGGAGCAGCTTG
Seq A exon
GTAAGTAACTGTAGTCATTGTAGGCAGTCTTTGAATTCTTTGTACTGTTCTTGGGATCTGAGATCGTTGACTCAAAAGTAGATATTATAGTGCAAAGATTGTATAAACTGAATCGTGACTTTTAAGTTGTATTAATTCAGCATGTACTTACTAGGTCCTTCCATGGAATCTGACCTCAGTATTGGAATCTGACCATGATCCAAGGACTTAATAAAATTTTAAAGGTTTGCTGCCAGGTAGCATGGCTCTTTTATGGTCAAGATTTATAATAGGGTTGAGCAATGATCATTCTTAGCTCGTCCCGCTGGCAGAATGTCTTCAGAGAGTTTGAAGTGAAGGATTTCAGTGATAGAATGAAAGAGCACTTTAAAGAATAGTCTGATGAGCTGATGGTTTTTATGCAAAATGAGAGAAAAGGCTTTTGTTTTGAAGGAAATATAAGCATATTGAAATTTTCCTTTAGTCCAGTTTGATAGGGAGCAGGCCCCTTTATAGGATAGATGTACTTTGTCACCAGTCTGCATTATAGAGCTGTAATTTCTCTAACCAGTGAGCTTCCCACGTGGCACTAGTAGTAAAGAATCCACCTGCCAGGTAGCAGACCCAGGTTCGATCCCTGAGTTGGGAAGATCCTCTGGAGGGGAGGGCATGGCAACCCACTCCAGTATTCTTGCTTGGCAGAGGAGCCTGGCAGGCCACAGGCCACAGGGTTGCAGAGTCGGACACGACCGAAGTGACCTAGCACGCACACGATACTCTTAACTAGGACAGCTGTGTAGCAAGGCATCCTGTTTTAATGTGTTAGTCTTTAAAGCTTGGTTTTGGTCAATGTTTTGTTTTGTGGGGTGTATGTGATATTTTTATCTGTCTTAATTTTGAGGAATAATAAATTATGGGCCAGCAGATGGATTTTAAAATGAAAGTAAGCTAGAAGAGGTAGCTTTTGTGGCAGAAAAGTTTGGCTTTTAAAGTTAGTCAGACTTGGGTTGGAATCGTTGCTTTGTTGCCTGTAAGCTGTGCAAATTTGGGCAAATTACTTAACATCTGAGAATCATTGATGTCAAATGGTCTTGTGAGAATTTAATCAAGTACAGTATACATCAAGTACCGCAGCTGGCTGTCTGTTTTCATTTATATAGAAATAGTTGCTTTCAAAGGGACTCTTTTTCATGCTAATTTTAAAGCAAAGCTTTGCTAAAATTATTTCAGCCTTTCAACCCTGGCCATTCTCCACAGGAGGGCTTCTATAATAGAGTCTAACTCTGGGAGCAGGGTAACACTCCCCCAAAGCAACCCAGTCTCCCTGATATCGAAGAGCTGAGGGCTTAGGGTTCTAGCTTAAAGATTTTATGTTTATTAAAGGGCACTAAAAGGACAAAAAGATTACATATATAAACATGAAAAAGAAAAAGGGATTAAACGTTACTAGATTACCTTCAAACCACAAGTAAGGCACAAGGGCTAGGACATAGGAGCTATATATTCAGAAAACATTTCACAGAAACCATATTCTGAGGGAAAAAAAGAAAAAATCCAGCCCCAATATTCATGGTATGTTCTGCCCATCCCTGCTGGGTTAGGTCAGTGTTTGTGCTTGGTTTGCATTGTTCGTGCCCCCTCCCTTTTTTAATTAACTTTGACCGGAGTACAGTTGTTTTGCAATGTTGCATTAGTGTCTGCTCTTCAGCGAAATGAACCAGCCATGCATATACACATACCCGCAGCCCTCTGGACTTCCTTCCCATGGAGGTCACCGCAGTGCGTCAAATAGAGTTCTCTGTGCTGTGTGTTCTCATTAGTTAGGCGTCTAGTTCTCAGGCCACTTCTGTGTAATGGCAGCTGCTGGTCTTCCTTTATGAAAAGGCTGGTGGGTTTGGGGGCCGGGGGGCGGTACTTGTGGAGTGATGTCATAATTCGTACTGAACACGTCTGTCCTCTTCTGACTCTGTAG
Seq C2 exon
GGCAGCTGGACACAGTGGACCTGAACAAGCTAAATGAGATTGAAGGCACCCTGAACAAAGCCAAAGAAGAAATGAAAGTCAGTGATCTAGACAGGAAGGTGTCCAACCTGGAGAACGAAGCCAGGAAGCAGGAGGCTGCCATCATGGACTATAACCGAGACATCGAGGAGATCCTGAAGGACATTCGCAACCTGGAAGACATCAAGAAGACCCTACCCTCCGGCTGCTTCAACACCCCGTCCATTGAGAAGCCCTAGCGTCTTCCTTAGGGAGCCACTGTGAGGCCACAGAGTGCCTGCACACAAAGATTACATTTTTCAGACCCCTGCCCCCCCCACTCTCTGCTGCTCTCCACCACTGTCCTATTGAACCAGGAAAAGTCACACAGTTTTAAAGAGAAGCAAATTAAACATCGTGAATCAGGAACAAAGGGTTCTATCTAATAAAGTCTCTCTTCCACTTAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011966:ENSBTAT00000015881:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.412 A=NA C2=0.471
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTTCACAGGCAGCTCAGGAAG
R:
GCTAGGGCTTCTCAATGGACG
Band lengths:
357-2308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development