GgaINT0024836 @ galGal3
Intron Retention
Gene
ENSGALG00000003580 | MMP2_CHICK
Description
NA
Coordinates
chr11:3694404-3696433:-
Coord C1 exon
chr11:3696278-3696433
Coord A exon
chr11:3694558-3696277
Coord C2 exon
chr11:3694404-3694557
Length
1720 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAG
5' ss Score
5.39
3' ss Seq
CCCTCTGTTCACTCTTACAGAAG
3' ss Score
10.54
Exon sequences
Seq C1 exon
GATACAGTCTCTTCTTGGTTGCTGCCCACGAATTTGGCCATGCGATGGGATTAGAGCACTCCGAGGACCCAGGAGCTCTCATGGCCCCGATCTACACCTACACCAAGAACTTCCGCCTTTCTCAGGATGACATTAAGGGGATTCAGGAGCTATATG
Seq A exon
GTAAAGTTGTCCCTCATCAGCAGAATTCATCAGAAATGTATGGAGCACAGGTTGAGTTTTGGGACTTAGAACTCGCAGTAGATGTCATAATGCACGATATCACAAATGCCAGAAACATCCTGTTTTTCCCTAGTTGCTCCATGGTACTACCAGGGGTCTTACTTTAAACAAATATCACAATTTAAGGATGAGGAGTCATTAAATTTATTGCAATAAACAGAGCCTCCAAACCCCCTGACAAATGCCAAGCTTTTACATTAAACTTTCTAGTGCCTTTCCCAGGACAATGAAATGCTGTGTTTTCCTCTGTCTTGAAATATCTGATGTGGGTATTTTGTCTACATAACCCTGATCTTCCTAGCTCATAACTCCGTGCAGGAGGGGAAGGGGCTTGTTTCCTGTCCCAGCTGGAAAAGAGTTCACACTGACTTCCCACTACTCAAGTTGAATAGTCACAATAACATTTGCAGATAATGTGTGGGAGATTATAGCTGTGTGTAAACAAATGTGGAAAGCTCCCGGATAAGTACTTTTATGCTTTTATCTTAAAATTCATTACTTTTTCCACAGACACTTAGTAAAATGCATAGAAATAATTATGATTGAAGGCCCTTCTGTTTATCCATTTTCCACCTTGTGAAGGCAAAAATATCCTACAGTCAATTAAGTGGTCTAGAAAAATCCACAGCATTTCTCTTTGTGCACTTCACACTTTTCCACCAGGATATCTTCCTATGACTATGTGGCACAGCATTCAGGACCTCAGAAATTAGTATAAGGATATATCAAAATGATTACCACATGAGACCTTCTTTGTCAAAAAACAGATTCAACTTTTTTCTTGTCTTTGTTCTTAGTTGCTTTAATTAAGACTGGGAATTAAGATGTTTGCAAGGTTAAATGAATTTTCTAAACTCACCCAGCATATCATTGATAGAGCTCAGAATTTAACCCAGTGCTCTCCAGTTGCACATCAAAAGCCAAGACAAAACCATGATGGTTCTTTGTAACTGAAATAATACTTAGACAAACTGCTTTTTATATAAAACAACTGTTCGGGAAAAAAAAAATTCTTCCATTACTGTTACCTCAAATCAGCTACTCGCACATAGTGTTTAACAAAGTTAATCAGTCTGATGTCTAAGGTAAGCCTCATAGCAACCAGAAAACAGAGAAAAATAAACCAGGCAGCAGAGAGCATGTTCTGAAAAGCACATTTTGGTTAGTGTTAAAGACACAAGGACCACACACAAACTCCTCAGAATTCATCTTTACAATCTGCAAAATATTAGCACTTGTAAAAAGAAGAAAAATGTCTCTCTCAGCTGAGTTGCAGAGAATTCTGAATAGAAGGACTTCAAAGTCCATTTCTCTTCATTCTACAAATCACTATAATAAAAACTGTAATGTTAACATTCAAACCCAGTATAGTCAGCCCTGGATCTTTCACTTAAATAGACAACTAAACACAATAGACACAGCTAGGTGCAGTATCTCAAATGGCGTCACAGCAGATTCAGGCAGGACTGGAAGCTAAGGCCTTCTCAGCTGGACACAGCCACCCTTCCTTATAAGACTTCATCAGAATTTTTTCCTCTTCAAAAACTTTCTCAAAGCTATTCCCTTGGATTAATTATGATCAGTCATGATCTGTGTTACAGATGCAGCACTGCATTACAGCATAATAGAACACCCAGAATCCCTCTGTTCACTCTTACAG
Seq C2 exon
AAGTATCACCTGATGTGGAACCTGGACCAGGGCCAGGACCAGGGCCAGGACCACGTCCTACCCTTGGACCTGTCACTCCAGAGCTCTGCAAGCACGACATTGTATTTGATGGAGTTGCACAAATTAGAGGAGAAATATTTTTCTTCAAAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003580:ENSGALT00000005666:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.481
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF0004514=Hemopexin=PU(36.4=30.8)
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:
GATACAGTCTCTTCTTGGTTGCTG
R:
ATATTTCTCCTCTAATTTGTGCAACT
Band lengths:
294-2014
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]