BtaINT0084092 @ bosTau6
Intron Retention
Gene
ENSBTAG00000027181 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr24:33176113-33177253:-
Coord C1 exon
chr24:33177109-33177253
Coord A exon
chr24:33176254-33177108
Coord C2 exon
chr24:33176113-33176253
Length
855 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTCGTGGTTTTCTTTGATAGGAA
3' ss Score
8.16
Exon sequences
Seq C1 exon
ATGCAGGCCCAGGATCACAGGGCGGCAGTGTGACCGGTGCGCTCCCGGCTTCTACCGCTTTCCTGAGTGCCTCCCCTGCCACTGCAGCAGAGATGGGACCGAGCCGGGAGTCTGTGACCCAGGCACCGGGGCATGTCTCTGCAAG
Seq A exon
GTAAGATGGAATGTGCAATGCTGGGGATATGGGCCACCGGCTAGAGTGGAGGGTCTTCATGCTGAGTCATTGTATAAAAATCTGTGGGAAATGAGACTGACCCATGATCAATGATGCTGGGAAAGATTGAAGGCAGGAGAAGGGGATGACAGAGAATGAGATGGTTAGATGGCATCACTGACTCAATGGAAATGAATTTGAGCAGGCTTCGGCAGTTGGTGATGGACAGGGAAGCCTGGCATGCTGCAGTCCATGGGGTCACAAGGAGTCAGACACAACTAAGTGACTGAACTGAGCTCATTGGGTAGAAACAGTTAGAAGCCATCCCAGCCTCACTGCTCTTGTCCTTTGGAGGGTCTACAGACCTCCTTAAGAATCTGATGACACAAATGGTCTCCAGAAAAATCGGCACAAACTTTTGTCTATAATTTGAAGAGGTTCATGGGTTTCCCTGAAGCCTATTCCTGTCCCGTGGACCCCAGGTTCATCATCTCTGCTCCACGGTGTTCTGCCAATGACAGATGGACTCCCCAATCCCAGCAGATGCTCTAAAGTGGTTATAAGTGGGATGAACCAGTCTCCCCCACATTGTGAACTTTTTGGTGCTGTTTTTCTACCTTCAAGATGCTAAAGGGTATCTGATGAAATTTAGGAAATCCTCTCTTCCATTTGTATGCGGTATAAAATTTAAATAGTTAATGTGGTAGAACAGTTGAACAGTCATATAACTTTGAGTGTTTTATTACCATCCATGTCCCATTGTCTTATGTTGGTACTTAATTTGTGCGTGTAGCTCTCTTCAGTCAGAGACCCTTCAGAAGGAATTATCTCTTCTCTCGTGGTTTTCTTTGATAG
Seq C2 exon
GAAAACGTGCAAGGCACAGAATGCAACATGTGTCGGGAAGGGTCATTCTACCTGGACCCAGCGAATCCCAAGGGTTGTACCAGCTGCTTTTGTTTCGGAGCCAGTCATCACTGTCACAGCACACTTAAGAGAAGGGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000027181:ENSBTAT00000060991:32
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:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)
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:
ATGCAGGCCCAGGATCACAG
R:
CTTAGCCCTTCTCTTAAGTGTGCT
Band lengths:
286-1141
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]