GgaINT0011774 @ galGal3
Intron Retention
Gene
ENSGALG00000005321 | LAMA5
Description
NA
Coordinates
chr20:7838547-7840517:-
Coord C1 exon
chr20:7840361-7840517
Coord A exon
chr20:7838686-7840360
Coord C2 exon
chr20:7838547-7838685
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:ENSGALT00000008535:23
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
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]