GgaINT0112317 @ galGal3
Intron Retention
Gene
ENSGALG00000007905 | LAMB1
Description
NA
Coordinates
chr1:15893104-15894252:-
Coord C1 exon
chr1:15894189-15894252
Coord A exon
chr1:15893307-15894188
Coord C2 exon
chr1:15893104-15893306
Length
882 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTTTCTGGTGTCCCCTGCAGACC
3' ss Score
11.78
Exon sequences
Seq C1 exon
GTCATATATCGTGTTTTAGATCCTGCTTTCAGAATTGAAGATCCATACAGCCCAAGGATTCAAA
Seq A exon
GTATGTATGCAGTTATCTTCTAGGCTCATTTGGAAGTGTTTCTGTACTTAGAGGTGTGATCATAAACCAGAAATGCCCATAGTGGGCACATAGACTCACTGCAAGCAAGGAAAGCAGAGAGATGTACAGACCTGTTGCTGTAGTGGTGTCAAAGTTTAACCTCTTTTGGCATTTGGCCTGAGTAGGGAATGGTAGTGCTTGGCTGTAAATCTGACCTTTAATTTTATTTTCCTTCTTAGCTTCAGTTCACATCCTTCTGTGTAAAGTGTGTAAACAGTAGTAGAAGAAAATATCTGAAGTAGAAGAGTGTCTGCTAGTTGCTATATTGGTTGAATATTTTTACCCAAATTTTTAAAGGAGAGAGAGGCTGCTTTCGTCAGCTTATTAAATTTGCTGGGAACATTGGATGTATAAGAAAGAAGAATATGTTTGTGTCTTGTTTCCATCTTAGATTTTTATTCAAAAGACTCTTAACTCTTAAAGGTCCAAGTCCACTTGTCAGCAGTTGCTTAATATTGACCCCCTCCCTTCCTCCTCTTATACTTTAAACCCCAAAGCGTCTAGAGAACCGGTGTCTCATCTGGTGGGGACTGGTATATGTGTCTTTAATATTTGTGCTCTTGCCTGTGTATGCCTGTAGTAAAACAAGCTAGTAGTTTTATTTAAGCTTAAAATAGCTTACACAGTATCAGCCTGTAGTAAGTTACTGTAATTTTTAGAAGTGGAGCATATGAAGTGGTATGATACGTAGCATGTAAGAGCTGAAATTAAACCTGATCTAATCTGCCCATAGGAAGTGTGTTTGGGAAGTCACTGCTGGCTTCCTCCCATTCAGTGTCTGGTAAATAACTCCAAAACATGTTTTTCTGGTGTCCCCTGCAG
Seq C2 exon
ACCTGTTGAAGATCACAAATCTAAGAGTCAAGTTCACCAAGCTGCACACACTGGGAGATAACCTCCTGGATTCGAGGATGGAGATCAGGGAGAAGTACTACTATGCCATTTACGACATGGTGGTGCGCGGGAACTGCTTCTGCTATGGCCATGCCAGCGAGTGTGCACCAGTGGAGGGCTTCAGTGAAGAAGTGGAAGGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007905:ENSGALT00000012832:5
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:
PF0005512=Laminin_N=FE(10.6=100)
A:
NA
C2:
PF0005512=Laminin_N=PD(18.4=63.2),PF0005319=Laminin_EGF=PU(35.5=32.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATATATCGTGTTTTAGATCCTGCT
R:
CCTTCCACTTCTTCACTGAAGCC
Band lengths:
262-1144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]