GgaINT0112337 @ galGal4
Intron Retention
Gene
ENSGALG00000007905 | LAMB1
Description
laminin, beta 1 [Source:HGNC Symbol;Acc:HGNC:6486]
Coordinates
chr1:14686740-14689089:-
Coord C1 exon
chr1:14688848-14689089
Coord A exon
chr1:14686944-14688847
Coord C2 exon
chr1:14686740-14686943
Length
1904 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
TGCCCTTGTCTCATTCCCAGATG
3' ss Score
10.16
Exon sequences
Seq C1 exon
GAGCCTTGGACAGCATCACCAAGTATTTCCAGATGTCCCTGGAGGCAGAGGAAAGGGTCAATGCTTCCACTGTCCACCCCGACAGCGCCGTGGAGCTGTCAGCGCAGACACGGCAGGAAGTGGAAGACTTAATCAATGAGAAGGAGGCCCAGTTCAAGGCTAAGCAAGAGGAGCAGTCGCGCCTCCTGGATGAACTCGCTGGCAAGCTGCAGAGCCTGGATCTCGCCGAAGCATCAGCAAAG
Seq A exon
GTATTTGGCTGAGAATTGCTGGGATAAAACCTACAGCAAAAAGTTGGGCTTGTGAAGAAGCAACAGGCAGGGAGAAGCTGTTTAGAGCTGGACAGTAGGAAATACAGTTTGTTCCTACAAAAAAGCACACTTCATTGATGATGTGCGGGCTCCGAGACACCTACAGGTTTTCAGGCATCAGCCCTTCATGTTGTTCTCCCTGTTGCTTCTAGAAACTGAGCCCTGACAGCACCTCTTCATCACATCCTAAGCCAAATCCCTTTGCTGTGGGCAGAGCTCTCAAGTGCAGCAAAATTTAGTGAGTCCACTGGACCGAGAGCCGACCTCTTAAATCTCAGTTAACATGCTTGCTTTTCCTGGGCTGCTTTGTTCTTGCAGCATTTCAGAGTCCCATACCTGTGCGGCGCTCATGCTCACGCTGCCCTCCTTGGTATTGCCACACTCCCATCCTTCTGCTTGAAACAAGGCAGAATTTAAAGGGAGCTGGAGTCAAAAGGGCACGGTCCCTGTTGAAGCTGCCTGCTCATCTGTAAATACGATCAAGGGTGGTTTTCTCTGGGGGCGAGGCAGGGTGTTCCTTCAGCTTCCCTTTGAAGGCAGCCGACTGCATTCAGAGAACAATCCCACTTGAAGTTCCACAGAAGGGAGAGCTCATTAACTCCTCTGGGCAAGGCTGGGCCTGCGGGAGAGGATGAGGTCTTCACACAGTGAATTGTCCCCGGTCCTTTACAATGACAACCACCCACCCCAGTCCTCTGTCTCCTTTTTCTTGGGGAGAGAAGAAAGAGGCATCTTTTTGTTTAGTTTCCCTGCCCCTGCATTCCTGCCTAATGTGTTCTTGAGGACCGAAAATCTTGGTTAGATGTTATCAGAGCAGTAAACACTGAGTTAGTTGCTTGGAGGTGTAATCATGGGATGCAGAAACAAAATCTTTTTGCTTTCTAGCTACTGCTGGGTTGTGTGCAAAGCAGGTAAGAGGGAATCCATTACACTTCACAGGAGCCAGCTGCAGCTAACTTGGCACAGCCCCTTGGTGTTCCCAGAGAGATTCTTGGCTTAAAGTACATCAGCTAGTGACTATCCTTTGGCATAAGGAGCGGGGTGGAAAGCGAAAAGAACCTCACAGGAGGAAAGGATTTTCCATCTGGCTAAAACAACTTCTAATGATTTCATTGTCCAGTTGACCACAACAGTGGATAAGCTCAGTAAAAATTGCCAATTAAAGTAGTTTTACTTAAAAAAAAAAACAGCAACAAAGTTGGTCTCTTCCGATTTCATTGTCACAAATTGGAAAGCAGTGTGACAGAACAAACATTCGATGGAAGGGAAGGGGACAGTTTTTCAAGAGAGGTGAAGAAGTTTCCTGTTCAGTATTTTATTTGTTTTCCTTTGCTCTCCCCCAGGCAGCAAAGGAAAAGAGCTTATCTTGTGCAGAACATATTCTTCTTTTTTAAAAAAGCTGCTTGGGTTAGCCAGTGTTTCCTCCAACAGTAACAAGACTGGCTTCCAACAGAAGGAATACAGGCAGTAGTAGCTTCCAGCTTGTAAACCAGAGCCTAAAGGCAGCTTTCTGGTGAAGCTGACAGTCAGGAAAAGCAGACAATGAAGGCACAGCTGCCCTCAAGCTACTCCAGCAGCTGGGAGCTGGCTTGTTGCAATCAAGTTAAAGGCAGGGAGTTGTGGAAAGGTCATAGAAGGACTACCATCATGCTGGTATGGACCTGATGCAGGAACCGTCTGCTCTGCTTCAGCATCATTTGCTATCATCGAATATCCCAAGTTGGGAGGGACCCATAAAGATGGTCAAACGTCTCAAGTTGTGCTGTGGTATTTAGGATGCCATCCCCCTCACAGCTCAGCAATAAAAATACAGGCTGTGATCACTGCCCTTGTCTCATTCCCAG
Seq C2 exon
ATGTGTGGCACTCCAGTGGGAGCCTCTTGTGCTGAGTCGGAGTGTGGAGGACTGCACTGCCGGACTGCTGCAGGGCAGAGAAAGTGTGGAGGACCTGGCTGTGATGGGCTGGTCACTGTCGCTCACAACGCGTGGCAGAAGGCCATGGACTTCGACAGAGACATCCTCAGTGCGCTGGCAGAAGTTGAGCAACTCTCCAGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007905:ENSGALT00000012832:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF150111=CK2S=PD(28.8=56.8)
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:
GGGTCAATGCTTCCACTGTCC
R:
GTCGAAGTCCATGGCCTTCTG
Band lengths:
344-2248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]