GgaINT0011774 @ galGal4
Intron Retention
Gene
ENSGALG00000005321 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr20:8206333-8208303:-
Coord C1 exon
chr20:8208147-8208303
Coord A exon
chr20:8206472-8208146
Coord C2 exon
chr20:8206333-8206471
Length
1675 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGC
5' ss Score
10.12
3' ss Seq
CCCTTTCTCTCTCCCACCAGCCC
3' ss Score
11.3
Exon sequences
Seq C1 exon
ACCCGTGCGGGACCATTATTTCCCTGACCTTCACCACCTGAAGTTTGAGCTGGAGGAAGGGACCACGCCAGCCGGCCGGGCCGTGCGCTTCGGCTACAACCCGCTGGAGTTCGAGGGTTTCAGCTGGCGAGGATACGCACAGATGTCCTCCATCCAG
Seq A exon
GTACGCTGGGTGGCTCCGTCCCAGCCCGGCTCCCCTTAGGGGAGGACACAGCCAGCAGAAAGCAGACGTGCTTTTGGCACACATCTGTTGCCCCAAGCGCTTCTCAGAGCCACGTGACAGCCAACATAAACAGCACAGTGTATATATAGCCTGTTTGTGGAGATATTTCCTGTAGTTCTGGGGGCGGCATAGACTGATGAGGGGAAAGATCCTAAACTGGGAGTCCCCTGACATCCTAATCCGGTCAGACAAAGGTGGTCGCTTGGCGATTGCTTACAGGGATGTCTATAAACACTGTCTCGGGGTTTCCTTGTGGCTATTTCCTCTGACTCTGCTCTTTCTTGCAACTTTCCGTGTAACCTTCTCACCCTCTTCCAAAAATAAAGCAGATTCTTTGCTGCCATATTCAGCTTAGACCTCAGCCTCGGCTCTTGCTGGTAGATGGTTTGCCATAACTATGACTTACACTAACCTGGAGTTGTCTAAGCCCCAGAGATGAAGTTGTTTCATCTGTTGACTCTTTTATTTCTCATTGGATTCCTCTTCTGCATGGCACCTGCTGAAGTGTCACCTGTATGTGCGTTTGGGGATGGAGTGCAGGACAGTTGTTCTCTGACAGTCTTGTCCCATTTAAGGTTCCTTATTCTGATATGTGTACTTTCAGTTTTCTTTACTTTTTTCACACTTAAGTGTAATAACAGAGAGGCCAGAAGCGTTGACTCTTTTCCATTGAATTTGTACTTAGGAGCTAGGCAGCAAACTACTGTAGGTGCCCTTGAGAAAACTCTAGCCTTAAAGTTTAAGGATGATGCTCAAGCTCTTGGCTTTGTTTTGCATCCAATGCTGGCACCAAGATAGAAATAGGCCTTGATAGAAGGGCAAGTTCATGGTTTTCTGCTGGCAGTTCTCTCCTGTAGTTTGCATTCTACAAGGTCTTTCCAGTTTGTTCTCCTGTGGGTGTATAACTGCTGCTCCCAGGAACACAACCCTCCTTGGGAGTCTCCCCAGGCATGCCCCCTGCTTTCCACCATAAGCAGAGGGATATTCAAGCAGGTGTTTAGATCTCTTTAAAATCAGTAGGACCTAAAGCATCTGTTTAACTCATGTCTTCCCATGCAGTATCCAGATAGGTGGAGGACTGATGCACACTCAGTGGCACATTCCCTCGGCACCAGTAGTTCGTAGCCTTGCAGTTTCCTGGGGATGAGGAATGAACTCCATTTGCAGCCTTCTCTGTAGGCATCTTATCAGAGATGTGGAAGCGCAAGAGCAGTGGCCTCAACATCTGCTACCTGCTAGCTGGTTATGTCACAAAGCCCAAAAGCATTATGTAGATAAGAAAAGCAAGGATTTCTTAAAACCTCTCCTCTGACTTGGCACGTGTACCAGGCTAGCCGAACAACCCTGCTGTGCCAGAGTACCTTCCAGACGTGGTCAGAGGCTTCCCACCCCTTCCCGCAGGCAGCTTGTGTGCTCTGCAGGCAGCCCTGGAGGGGACGGCATCATGAAGTGCCTGTGCTGGGGCTGTAGGGCCAGGGTGCTTGTCTTCTCCTTGCTCTGTGGCATGTCGCTTTGGGAGCAGTGAGCCAAGCGGCTGCGCTTGGGCTGGTGGCTGTCAGCGGTGGAGGTAATTGAAGGTGTGCTCTGCTTCTCTCCCCTTTCTCTCTCCCACCAG
Seq C2 exon
CCCAAGGTAGTGGTGACTCTCAATGTGACCTCCCCCGACCTCTTCCGCCTCGTCTTCCGCTACGTCAGCCGGGGGTCCGCCATTGTTGAAGGGAGGGTCTCGGTCGTTGAGGAAGGAAAGTTTAATATTTGTGGCAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005321:ENSGALT00000008535:18
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(21.4=17.0)
A:
NA
C2:
NO
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:
CCGTGCGGGACCATTATTTCC
R:
AGTTGCCACAAATATTAAACTTTCCT
Band lengths:
294-1969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]