GgaINT0046549 @ galGal4
Intron Retention
Gene
ENSGALG00000003578 | fn1
Description
fibronectin precursor [Source:RefSeq peptide;Acc:NP_001185641]
Coordinates
chr7:4336533-4338300:-
Coord C1 exon
chr7:4338162-4338300
Coord A exon
chr7:4336698-4338161
Coord C2 exon
chr7:4336533-4336697
Length
1464 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTCTTCTCTTTTCGTTCCAGTGT
3' ss Score
10.18
Exon sequences
Seq C1 exon
TTCAGGGTTCCTGGCACTTCCTCCAGTGCTACGCTCACTGGCCTCACCAGAGGTGCCACCTACAACATCATAGTAGAAGCCCTGAAGGATCACCGCAGACAAAAGGTGCTGGAGGAGGTGGTCACAGTTGGCAATACTG
Seq A exon
GTAAGTGAAAGTTTTATGAAGTCTAGGTGAACCTTTGCTGTACCTGCCTTGCTTTCTTTACTCCAGCTCGGGCTCCAGGTGGGTTGCACTGAGAATAGTTCTGAACGAAAACTTGTGCAGACATGGAGAGTTTGTAGGAGGGTACTGGGACAAGTGGTTTGTGAGTCCCATCGGTTTTGGATAACCAGCTCACACTGATTGTGTGACTTAGAGCTGTTCTGATCTGTTGTCTGATCATGAAGAATGTGCCTTGAGGCTCCATACCCTCCTCTAAGGTCTGTGCTGGAGAGAAAGCAAGAGATCTGGTGTTTGCTGCTCTCACAGGAAGCCAGGGATCATGCTGGTGTTGCAGATTCCTGCCCACCAGGGAAGACTTGCTATCACAAGAACGAGGCATGCTTAAGGGAAGACGCTGGAAGATAACTGCTCTAACAGTCATTTGCCACTGCTTCTGTGCTGGTTATCCAGCAGCACCAGCAGACGGTCCTGAAGGTCTGGCAGTGGGGCAGGCTGCCTACAGAGATGCTGATTAAGCACAGACAGGCAGCACTTAGAAGCCTTGTGACCAACCACAAGTATGTGTGGGCAGAGGCAGCCCTTGCCACAGCTGGGAAGCCTGGAGCCCACACACCCTGTGGGACCCAGGCTTTGCTTGTGGCCACACGGGGATCTGGTCAACAACCCTCCCTCCTTCATTCTCATCTTGTGGGTACTTTAAGGTCAAAAAGAAGAAGATGGGAAAAAAAGGAAATGAAGAATTAAGGATTTATGCTGTTCACCCCATAAACTGCTCCATGCATCTCCCTGCTGCCCCCACTTCCCTGGGGAGGGAAGAGAATAACTGGGAAGACTATTTTTCTCCTTCCAGCAGCCCAGCTGCCTTCAGTCAGTTGCAGACAGTCTTGCCTCTGATCTTGATTCTTGTCTCTGGCCACCACACACTGAACCAATGGTTGTAAAACACCTTTTTGATCAAGGCACACATGTAGGGTGGAAATCTGTCTTATCTAACAGCGTGGCTGTAAGTCTCTTTCCACCCTCCCACCCTGCCATGAGCTACAGCCTGAAACACCTCCAGAAAGCACCCATGCAGCCACCAACCCCCAGCCTCTCACAGCACACTTCTCATAAACAGACTAAGTCAGGTTGCTGCTCTTCACCAGCCGGTACAGAGTCTCACACTTGCTTGAAACTTGGCAAATCAAAATGAAAATAGCCTTCATGTCAGCTTTTTTGTTTTTTTTTTTTTATCATTCCACTGCTCTGACACATGCAAATGGAAAATAAATCGCAGGGAGTCTGAACTGCTGATAGAGCCATCAAGTGTATGCCCATGGGGTAGTTCCATTACTAGCAGGATATTCAAAGGAAAAAAAAAACAACACGTATTCAGTGAAAATGATTCTGCCTTTCAGTGGCTCCTATTGCTGTGTGTGATGCCTGTTTCTTCTCTTTTCGTTCCAG
Seq C2 exon
TGTCTGAAGGACTAAACCAGCCGGCCGACGACACCTGCTATGATACTTACACTGGCTCCTTCTATTCCATTGGCGAGGAGTGGGAGCGATTATCTGAAACGGGCTTTAAACTCTGGTGCCAGTGCTTAGGCTTTGGCAGTGGTCACTTCAGATGCGATTCCTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003578:ENSGALT00000005663:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.036
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(42.9=70.2)
A:
NA
C2:
PF0003913=fn1=WD(100=71.4)
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:
GTTCCTGGCACTTCCTCCAGT
R:
GGAATCGCATCTGAAGTGACCA
Band lengths:
294-1758
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]