GgaINT0081918 @ galGal4
Intron Retention
Gene
ENSGALG00000015001 | LAMA4
Description
laminin, alpha 4 [Source:HGNC Symbol;Acc:HGNC:6484]
Coordinates
chr3:65168844-65170367:+
Coord C1 exon
chr3:65168844-65168939
Coord A exon
chr3:65168940-65170215
Coord C2 exon
chr3:65170216-65170367
Length
1276 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGA
5' ss Score
5.52
3' ss Seq
CACTTTTATTTTCTTATCAGGCT
3' ss Score
7.83
Exon sequences
Seq C1 exon
CATGTAACTGTGGTGGGAGAATGTGTGACAGCCGGACTGGAGAATGCCTCGCAGATAGTCCTCTAGTTTCTACTGGCACAGACTGCCCAACCATCA
Seq A exon
GTAAGAATAACATTATGAGAACACCAGAAATGAAGATCACTCTCAGATGCTTGCAGATGCTAACTTAACAGCTCAGCTCTCTCCAGTGCACACTCGTACCTTGGTTCTGCAGGGCACTTAAACATGCAAAGATGCAGTGCCCTACTGACTGTGTATTTTAATTCATACTTACCTGCCTGACTGAGCCCATGAATATGTTCAGCTCTGTAAAACAGGCTGTATGTTTAGGTACAAATTACAGAGCAGTATGGATGTATCATGAAAGCTACTTCTCTAGGCCTAGAGATACAGAGCCCGCAAAAAAAATTCTCTAACCCTAAAATGCCACCTTGCATATCATTTCTGTTGTTCTCATTTTACATGAAATATAAACTGTTACTGTTGAATTTGACATACACACATCAGTCAGTTGTTTTTCAGCTGTCTGCCCTATTCTAAATACAGGAAGCCTGGGAATTTTTCAAAAGCGCTGTTATAACTTCTAGTGAATACTGAAACTTTTAAAAAGATAGTATTAAGGCTATAGTATTATACAGTCTACATATCACCTACGGACTCCTAAGCCTGTTCCCAAGAAGAGGGATCACATGTCCAGAAGCACAATCAGGAGGAAAACATTTGGCAGCTGCTGCCATCAGGAATACAGACTGTACAATACCAAGCAAAAGTTCCTGCAGGAATCTGTATTTCATATACATATAAGTCTCCTGCACTTACCGGTGGCACAAATGTCACTAAAAACAAGGTGGTATTGCAAGCATTCATACAGGACAAGGGTGTAGTTTTACAGTAGCATAGTTCAACATGTCAAAACTCTGCCTTGAGAAGTTGCCATTCTAATCATATAGACAGCCAAGAGCCCGGTTGATGGACATCCTTGCTTGTCATACCACCAGATTTAGAATGCAGAGTTCTGACTGCGGGCAAAATGAACTTGTTTTTTTGACCCCCATCTGTTGTTCTTTAGGACACAAACAAGTGGAACCTCTAGGGAATAGCCAGGAAATGCTTCATCTCCTGCTCCCTACTGATAGCAGTGCCGCCTCAATGGCCCTTCAGAGCAGTCCCATCTGGTGCTGCTCAGCTGGAAGCATCGTGGCTGTGCTGTGGGACCTTGGGAGTGGGTGGATGAAAGGAAAAGAAAAATGGATATAAATCAAGGCCCATCCATGTCAGAATGAGGAAACCCCATGGGGCACTCAAAAGTAAATTTAAGATGTTGTTGTTACGTTTCGCAAGCACTAAAAGTAAAATGACACTTTTATTTTCTTATCAG
Seq C2 exon
GCTGCGATAAATGTATTTGGGATTTGACAGACGACATCCGGTTAGCTGTCCTGGCTATTGATGAAAGCAAATCAACTTTATTGAGCATCTCTACAGGTGTTGCAGCTCAGAAACGCTTGCATGACCTGAACCTCACTACTACCCATCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015001:ENSGALT00000024193:6
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(1.8=3.0)
A:
NA
C2:
PF060089=Laminin_I=PU(11.7=60.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTAACTGTGGTGGGAGAATGTG
R:
CTGGAGATGGGTAGTAGTGAGGT
Band lengths:
246-1522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]