GgaINT0123649 @ galGal4
Intron Retention
Gene
ENSGALG00000000182 | FGA
Description
fibrinogen alpha chain [Source:HGNC Symbol;Acc:HGNC:3661]
Coordinates
chr16:18284-20259:+
Coord C1 exon
chr16:18284-18437
Coord A exon
chr16:18438-19440
Coord C2 exon
chr16:19441-20259
Length
1003 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
GATTTCCTTTGTTTTCACAGTGC
3' ss Score
8.53
Exon sequences
Seq C1 exon
GATGAACCAGCAGCACTGACCACCCATGAGCTGCCTGGATCTGCAGTCACCTTTGAGGTGACAGGGCTGACACCTGGACAAGCTTTTGAGATCTTCATCCAGGCCCAGCGGGAGCAGCACCTTGGGGCGCCGGGCACGCTGCGTGTCCGCACCT
Seq A exon
GTATGTGCCACCTGCTGTGGGACAGGCATGGGGACAGAAGGGGCATGGGGTAGCATGGGGAGGCATGAGAGCAGCAGGGGTTTGGAAGTGGCATGGGGAGGCATGGGGACAGCAGGGTATGGAAGTGGCATGGGGACAGCAAGGGGGACAGAAGGGGCATGGGGTGGCATTGGCACAAGAATGAGGGCAGAGATGACATGGGAGAGGGACAGCATGCATGGAGACAGCATTCAGCACAGATGTGGGAATGAGCATAGCACAAGGACAGGCATGGGGACAGGAATAATGCAAGCACAAGGGTGGGGACATCATGGGCATGGGGTTTGAGGTGGGGACAGGGATGAGTGAGGTGGGGACAAGCATGGAAATGAAAATGGGATATGGACAGGGATGGGCATGTCACAGCTAGAGAGATGGAGGAAGGAACAGGCATGGGGATAGGGATACGATTGAAGGCAGATGGGGCAGGGATGGGTACTGGAATGGAAGTGGAGACGGGTGGTGTCCACAGCCTCTGTCTGTCCCCACGTGTCTTTATTGTTCCCATGGCTCTATGGGTCCACATGCATCTGTCTGTCTTGCAGAGGTCTGTGTGTCAGCAGTCTGTCCCTGTGGGTCCACATGTCTCCCTGGGCCTGTCCGTCTGCATCTATCCCCATGGGGCCGCGTGTCCCATGGGCTCATCTGTTCACTTGGGGCCTTGTGTCCCTTCAGGTCTGTGTGACCCCAGTCCATCCCCATGTGTCCCTGTGGGTCCACATGTCTCCACATGTCCTGATGCTTCCCTGTGGGTCCCTCTGTTCCTATCTGTCTGTCCTAGTCTGTCCTCATGAGTCTGGATGTCTCCAGGCTCTCCCTATGGTTCCCAATGTCCACAGTCTGCCCCTAGGCATCTGTTTGTCCTCCTCTGTTCCTGTGTCCATCCATCCCTGTGTCCCTGGGCTGTGGCAGATGAGGGATTTTGGGGACAGGGTAGTGACCTGGATTTCCTTTGTTTTCACAG
Seq C2 exon
TGCTTGCCCAGTCTCTGCCCAACCATGGGGGGCCACGGGGGACCCCTACATTTCTGGCATCTCCAGTGGCCCCAGCATCACCATCAGCCCGACAGTCTCCAGCATCCCCATGGTCCCCAGTGTCACTGGGGTCCTTGGGGTCACCAGCATCCCTGAGGTCTCCAGTGTCACCAGAGTCCTCAGCAGCACCAGCTTCCATGGAATCCCCATGGTCCCCAGCATCCCCACACTCCCCAGAGTCCCCAGCATCCCCAGTGTCCCCGAGGTCACCTACATCTCCATGGTCCCCAGCATCCCCACAGTCCCCACTATCTCCAGCATCCCCTATATCCCCAGTGCTCCCAAATGTCCCATCCCTGCATGAGCTGGGGGTCAAGCTTTCTTCCTACAATGGGTCCTTGCTGCAGCGCCTGGAAAGCCACCTCCGGGCCACCAATTTCCCACTCCGAGGCAACCAAACAGTGCCTGCAGTGGCCCGTGCCATCCTCTCCTACCTGCTTCGCCGCAGCCCAGCCTCACTGCGTTATCAGTTCCTCCGCCACCTCCAGCAGAACCCCCACCCCAAACCCCAGGTGTTGCCAGGGGCTGCTGGTGAAGCCCTGGTGGACTTGGATGGGCTGAGGGGTCACGCGGAGACAGTAGTGATCCGCTACCGGCTGCTGGAGGAGCCGGAGGGGGATGAGGGGGAGGTGAGGGTGCCAGGGGACACCACAGTGGCCCGGGTGCCAGGGCTGGTGCCAGGGGCCACATACCGGGTGGAGGTGCACGGTGTGGTGCGGGGACGTGTCTCCAAGTCCTACACTTCCCTGGTGACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000182:ENSGALT00000000238:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.437 A=NA C2=0.609
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(54.3=84.6)
A:
NA
C2:
PF0004116=fn3=WD(100=24.5)
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:
TGAGATCTTCATCCAGGCCCA
R:
TGGAGATGTAGGTGACCTCGG
Band lengths:
349-1352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]