DreINT0068095 @ danRer10
Intron Retention
Gene
ENSDARG00000020741 | fga
Description
fibrinogen alpha chain [Source:ZFIN;Acc:ZDB-GENE-031010-21]
Coordinates
chr1:9381989-9383935:-
Coord C1 exon
chr1:9383077-9383935
Coord A exon
chr1:9382857-9383076
Coord C2 exon
chr1:9381989-9382856
Length
220 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAC
5' ss Score
5.99
3' ss Seq
GGTGTGTAATCTTCTTTCAGATT
3' ss Score
8.46
Exon sequences
Seq C1 exon
GTTGACATTGACATCAAACTACGCACATGCAAAGGCTCTTGTGCCAGCTACAGCGAGTTCTCGGTGGACAGGGAAAGCTATGTGACTTTGGACAAGCAAATGGACAATCTGAACGCCATGCGTGTACAGAGCGTGGAGACTGTCAGTTCCTTGGGAATCATGAAGAGCAGGCCGTTGAAGGATGTGTTGGTGCCCACCATTTATAAGAGCGGAACGGGCAAAGCTGAGCAGAAGCTGCTTTTTGGAGATGTAGGCCAGATGCAGCTCTCTCTGGAAGCTGAAGGCTCCACTGCCGAATCTGCCGCCACAGTTAGCAAGTTTCCCACATCAGGTACGGGCTCCACATCACAAACCTCCAGCAAGCAGTGCACCAAATCAGTTCGCAAAGTGATAACACACACCAAAGATGGCCCCGTGGAAAAGGTTGAAGTTTCGTCTAGCGGGCCCGGGTGTGATGATTTAGGAAAACTAGGAATTTCAGATTCAGAGTTTTTGACGGCAGCCAAAGATGGGAAAGATTTGAGTCGCGATGGCTTGAAAATAACAGTGACCGGCGGTGATGAAAAGTCCCTCACTTCTCTAAGCCACAGCACTTCTGATCTGGGTGGCTTCGGAGGAGACTTCTTTAAGAATCTTGGCACTGACAACCGAAAGTATGCCTCATCTTCATCCTCAACATCCACAAAGACAGTGTCAGATGGAAGCAAAAGTTACTCAAAGACCACCCTCACTAGCGACCCTATTTTTGGGGATGACCTCGGGGCGTTCATGCGGGGCGACGTGGAAGAAGATATGCCCGACATCCATGCACGCAGTGTGAAATCGCAAGACGATCGCAAGGCTGGCTTTGTTGGCGGAG
Seq A exon
GTACACTCGAGTGAAACTCTTAACACAAGTGAACCATTGATAAACATAATGATAACACTATTAACAAGAGTTTGTTGGAAACATGTGGACTAACTGATATCTAAGTAAATACCAATCCATCACATTTATTAATACTCACCAAGAAGCAATTGTTTGGATCTCTGGAATGAATTTGCAATGCAGTTTTGCTCTAATCGGCAGGTGTGTAATCTTCTTTCAG
Seq C2 exon
ATTGCGTTGAAATCCAGCAGAAGCATGTGAACGGCGGTCAGAGCGGGATGTTCAAAATAAAACCAGCGGGGTCTGAGGAGGTAGTAGAGGTTTACTGTGACCAGAGCACTGGGTTGGGGGGATGGACTCTGGTTCAACAGCGGGAGGACGGGTCTGTTAACTTCAACCGCACTTGGAAGGAGTATCTAAATGGTTTCGGACAGATAGACAAGCAGGGTAAGGGCGAGATCTGGATTGGCAACAAATTCCTGCACCTTCTCACTCAGAAAGAAAGTCTTCTGAGGGTGGAGCTGCAGGACTGGACTGGAGCTGAGGCCTACGCTGAGTACAACATTAAAGTTGGCTCGGAGGCTGAAGGTTTCCCGCTGACTGCATCCGATTATGATGGGGATGCAGGAGATGCGTTAGTGAGAGGACATCCCAACCTTGGATCCTTCCTTTCACATGCTGGCATGAAGTTTAGCACCTTTGATAGGGACAGTGATAAGTGGGAGGAAAACTGTGCAGAGATGTATGGTGGAGGGTGGTGGTATAATAACTGCCAGTCAGCCAACCTCAATGGCATTTACTATAAAGGAGGCCAGTATGACCCGGCTACCAAAGTCCCCTATGAGATTGAGAATGGTGTCGTGTGGCTGCCTTTCAAACCAGCTGATTACTCCCTCAAAGTGGTGAGAATGAAGATCAGACCTGTCTGAAATGAAAACATAAAGAGGGGATTAGGGGAAAAAGGATGGATATCTGTTGTTTTGAATGAGCTGTATGATTAATATTCTGCTTGTGTTGAACGTAATACAATGATGATGCAACATACATTTTTACACAACCAGATTACCTCATGTTTCCAATAAAGATGTGTTCACTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020741:ENSDART00000033118:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.387 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF087025=Fib_alpha=PD(15.6=8.0),PF039997=MAP65_ASE1=PD(46.9=18.5),PF121603=Fibrinogen_aC=WD(100=24.0),PF0014713=Fibrinogen_C=PU(1.3=1.0)
A:
NA
C2:
PF087025=Fib_alpha=PD(15.6=7.9),PF121603=Fibrinogen_aC=WD(100=23.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATATGCCCGACATCCATGCAC
R:
ATCCAGATCTCGCCCTTACCC
Band lengths:
304-524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]