BtaINT0084088 @ bosTau6
Intron Retention
Gene
ENSBTAG00000027181 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr24:33204842-33206791:-
Coord C1 exon
chr24:33206676-33206791
Coord A exon
chr24:33205054-33206675
Coord C2 exon
chr24:33204842-33205053
Length
1622 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
GTGTGTTCTTGTTCCCACAGCCC
3' ss Score
11.26
Exon sequences
Seq C1 exon
GTCCGTATCCTAGTGGTGCCTGCAGAGAATTACGACTACCAGATCCTTCACAGAAAATCACTGGACAAGTCATTGGAGTTTGTCACCAATTGTGGAGGAGACAGTTTTTATATTGA
Seq A exon
GTAAGTATCACTTTGTGTGAGGGCTTCCTGGATGGCAGTAGTGGTAAAGAACCCGCCTGCCAATGCAGGAGACACAAGAGAAGTGAGTTCAATCCCAGGATAGAGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCCTTATTCTTGCCAGGAGAATCCCATGGACAGAGGAGTCCTTAGGGTTGCAAAGAGTTGGACATGACCGAAGCGACTTAGCATGCACACATCACTTTGTGGCACGGCCATGGGAGGCCTGAGGCTCTCCCACATTCCCGACCAGAGCAGGAGGCCTGGGGAGGGGTGGCCTTCGGGTCTGTCTTCCTCCTCTGAGCGCCCAAGGGAGCAGTAGTGAGTTCCTGCAGCACACGCTGACCTGTGTACTATCTCATCATGTCCATCTGGGTGGGATTTCCCTCTTCAACTCTGATCTCAGCAGATCACCCCCAAGCCGGGATTCACAGGCTGTTTGGGGGTTTCTCTTCCTCTTTGTTGCTTCCTGTCGGCCAACTCGGATTCCTGAAAGATACCACACAGGGTTTCCTCCGCTGTAGGGCACATCAGCCCTGATTCCCGCTCTCCTTTGCACTCTCATCAGTGGGGAGCATTACAAAGGGCTGGGCCTCCCTATCCTCCCTTGGTGGGTTCCCAGACGCTAAGAGCCTAGAACAGCCCTTAGTTTCAGTTCCTGTCATTCTTTCCTGCAGACCCCTCCTCCCTGCCCCCTTGTAGGTTTCCTGAGGAACCTGGGCCTCCAGAGGGTGGAAACCTCTTGTACAGAAAATATGAAGAACAAGGGTTCTGAGGTCAGACCACTGTGGATTTGAATGCCTACCCCACCCTCCATAGCTCTGTGGCCTCAAGAATGTTGCTTAACTTCTAGGAGCCTTAGCTGTCTTACCTGTGAAGTGGGGCTTTGGCCTAATCGGTTAGGTGGTTGTCAGGTTAACGTTGTTCAGTCACTAAGTTGTGACCAACTCTTTGCGACCCCATGGACTGCAGCATATCAGGCTGCCCTCTCCGTCACCAACTCCTGGAGTGTGCTCAAATGTCCATTGAGTTGGTGATGCTATCTAACCATCTCATCCTCTGCCACCCCCTTCTCCTTTTGCCTTCAATCTTTCTTAGCATCAGGGGATTTTCCATTGAGTTAGCTGTTACCGTCAGGGGGCCAAAGTATTGGAGCTTCAGCTTATGAGGTTAATGAGGTGAAGGGAAAACTTTTTAACATACATGTTCAGTAAAAGTTGACAATTCACCTCCTCCTCATTATTATCCTAGTTGGTATATCATAGCACATGCAGGTATAAATTTTTTGGTGACTGCTGTATTGAGATAGAACCTATACACCGTACAACTCATCCTATAGATGAATCTTCACCCTTTTATTCCAGCCACCAAAGGTTCCCACCCACCAGTCCTGTGATGAGTCCTGAAGTAGATGGGGGTGGGTGGGTGGCTGTCAAACACTGTAAGTCCAGGGGTGGGGTTTCCTCTCACTTTTTCCTAGACTCCAGAGCCCCTCTCCCAAAACACTGCTTGCTGGGGCATGGGGAAGGGGAAGGTGGGACCATTTCTGGGCATGCCTCCCAGGATCTCACTGTGTGTTCTTGTTCCCACAG
Seq C2 exon
CCCCCAGAGAGCCTCTGAATTCTGTAAGAATTCTGCCAGATCCCTGGTGGCCCTTTACCACGAGGGTGCACTGCCTTGCGAGTGCCACCCTGCTGGGGCCACCGGCCACCCCTGCAGCCCCGAGGGCGGGCAGTGCCCGTGCCGGCCCCACGTCATCGGGCGGCAGTGTACCCGCTGTCAGACGGGCTTCTACGGGTTCCCGCACTGCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000027181:ENSBTAT00000060991:29
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005319=Laminin_EGF=PU(91.8=62.5)
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:
TCCGTATCCTAGTGGTGCCTG
R:
CCGTAGAAGCCCGTCTGACAG
Band lengths:
310-1932
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]