GgaINT0024838 @ galGal3
Intron Retention
Gene
ENSGALG00000003580 | MMP2_CHICK
Description
NA
Coordinates
chr11:3687020-3689113:-
Coord C1 exon
chr11:3688977-3689113
Coord A exon
chr11:3687180-3688976
Coord C2 exon
chr11:3687020-3687179
Length
1797 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TTGTTTTTTCTCTTTCTTAGGAA
3' ss Score
12.03
Exon sequences
Seq C1 exon
ATTCATGTGGAGGACTGTAAACCCTCGAGGAAAACCCACAGGTCCTCTTCTCGTTGCTACATTCTGGCCTGATCTGCCAGAGAAAATCGATGCTGTCTACGAGTCCCCTCAGGATGAGAAGGCTGTATTTTTTGCAG
Seq A exon
GTACTGTTTTTAGTTTTAAAATATAATTATGCATTTGCATAAATGCTGCATTCAAGCTCAAGTTACTCTGAGTTGTAACTGGGCCAGGGAACAGCCTGACTGAGAGTAAGCATAGCCAGTGGGTACGGGCAGCAGATATCAAATATCCCATGCTGAGGACATTGCATCAAAGGCTGGATCTGAAAGGCTCTGAACAGCATACAGCCACCATTACAGCAAAAGGGAGCCAGTAGCACCCGGAAAGAAGCATTCAACAATAAGCAGGACTAAACAAGAATTATTACTTAATACACAAAGCAACCCAACATCCATTCTTGCGTTATTTCTTTCTGTTTCCTCTCATGATAAGCTATTGTCTCTGTGCATGTTTCTTGGGAATATTACGTCTTCTGTTCCCATGCCTCTCCTCTTCTCCTTTGCCAAAGACTGACTTCTACTCTGGCATCCAAGGATCTGCCTTGGTGGCTCACCAGCAGAGGACAAAGGGGCCATGCTCACTGCCTGCACCAGAGGGAGGAGATTAGGCAGCCCTGCTCTGGCCATCCGGAGTCACACATATGGTTCAGCTGTACCATCCAACTTAGCAGAGCTGGGCAGCTGTTTTCAACATGAAAAACTGAGCCAGCAAAAACTAGGCTCCAAACCAACCACCAAAAACATGACTAAACATCTCCAGTCATATAAAAACCACATGGCCCACGCTCCTGTACATTCTCTGTACAGGACGGAAAAGAGTAATGGTAATCTATTCCATATGTCTCAAAGGCTATTTCCTTTAGTTTACATGGGAGAAAAAAAGCTTTAAGATGTTTTATTTCAGCCAAGTCAAAACACTTTAAAAGTTGGATATACTATACCTAATCCTATTACATGTGCATCTCTCTCCTTTTCTTTATATTTTCCAGAAAAAAAATATAACTAACCTGCTTTAAATAAGAACTATTCAGACTATCAAAGGCTGGTTTGAAAGTTGCCTGTAACTATTTGTAAGTGAGAACCATGCTTTGCTTCTGAATGGTGAAGTGGCAACTTCTCAGGAGCTCAAGTGCTACATTTTATAGCTTTCTTATATTAAATGCTTTCCTTCCCACTATCTGTGTCATAGAATCCAGGAAATATCCTTTCATGAACAAGTCTTTCCATGGCTTTCAGTGAATCTTATTAGGTGCTTACTAAGTAAGTTACAAATCCATGTAAGGAATGTAGAAACAGACCTCTTCCACCACAACGTATTTGAAGAGAAATTAGAAAATGTCATGACAAAAAGGACAACACAAATATGAATTCTGGGCAAAAACTTCCTGGTAACAGCTCAATAAAGTTGCTGAAGAAAACAAACCAAGGAGACAAATTGCTGAATAAAACAAATAGAGGGCAAGCATGAGTTTCTGCGTTTGACCCGTGTTGATCCATGTCTGGTTTCAGACCATATTTATCACACAGAAGATTACCAAATAGTAACTGTATGTTTTACAATACCCAAACCATGCTTTTTAATTTCTTTCTTTTTTTAAAGAGCTGCACATTTGGCAATCTCTTTGGCTCAGAGCTCAGAAAAATGAAACAGACAAGAAATAGGAAGCAAAAGCACATTGAAATGATACGTATTACTGAGAGGCAAAAACAGAAATTGTGATCTCAGTACATCTGCACTCTAATTTAGTATGTCACAGACAGAAAAATACTAGAAAGACGAGTAGTACAATTAGTACAATAAAAACTGCCATATCCAAGTGTAAAAGAAGAAATATTCCTATGTGCCTGATTAATAAGCAGTTTGTTTTTTCTCTTTCTTAG
Seq C2 exon
GAAATGAGTACTGGGTTTATACAGCCAGCAACCTGGATAGGGGCTATCCAAAGAAACTCACCAGCCTGGGACTACCCCCTGATGTGCAACGCATTGATGCAGCCTTCAACTGGGGCAGAAACAAGAAGACATATATTTTCTCTGGAGACAGATACTGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003580:ENSGALT00000005666:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(61.4=57.4),PF0004514=Hemopexin=PU(38.6=36.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(59.1=48.1),PF0004514=Hemopexin=PU(45.8=40.7)
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:
TCATGTGGAGGACTGTAAACCCT
R:
TCTGTCTCCAGAGAAAATATATGTCT
Band lengths:
287-2084
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]