BtaINT0094014 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020676 | MMP9
Description
Bos taurus matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) (MMP9), mRNA. [Source:RefSeq mRNA;Acc:NM_174744]
Coordinates
chr13:75471821-75473824:+
Coord C1 exon
chr13:75471821-75471924
Coord A exon
chr13:75471925-75473510
Coord C2 exon
chr13:75473511-75473824
Length
1586 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GGCCACTTTCTCCCTTGCAGAGA
3' ss Score
9.7
Exon sequences
Seq C1 exon
GTTCGACGTGAAGACACAGAAGGTGGATCCCCAGAGCGTCACCCCCGTGGACCAGATGTTCCCCGGGGTGCCCATTAGCACGCACGACATCTTTCAGTACCAAG
Seq A exon
GTGAGGGCTGAGAGCCAGGGTCAGGGGGAGGATCCCTCCCAGAGATACCTCCCACAGTAGGTTCCCCTACCCTGTGTTGTTAGTCGCTCAGTCGTGTCTGACTCTTTGTGACTCCATGGATTGTAGCCCGCCAGGCTCCTCTGTCCATGGAATTCTCCAGGCAAGAAAACTGGAGTGGGTAGCCATTCTCTTCTCCAGGGGATGTTCCCCATCCAGGGATCGAACCCAGGTCTCCCACATTGCAGGCAGATTCTTTACCATCTGAGCCACCAGGGAAGCCCCTGCCTTAGTGATTGGTCAAATTTCAAGCCAGAAAGAAAAAGCCGGTGGAGACTGAGGCAAATGTCCCTCATTGATGAGTTCCCCGCAGAGTCAGGGATTTTCCCAGACCATTTGAGGACCAGGGCCACAACAGAACTAGAACCCAGATTTCCTGCCTCCCAGCTGGAAGCTCTTTCCCCCATGGCACAGGACACCTGGTTTGTATGAAGGCTTTATTAGACCATATTTATCAAGTGCCTGTAATATGCTAGGCATCACGCTGCCACTGGGGATACAGTGATAAATAAGACATTACATAGATGTGTGTGTGTGACTTTGGGCAAGTCACTGCTATTCACAGAGCCTCAGTTTCCCCATATGTAAAATGGGGATAGTAGCTGGAGTTAACCCTTTCTTTCTCTTTCCCACTGCTCACCCCCAATCAGCGGACAACTGCTGTTGGCTCAGCCACCAAAATATTTACAACCTCCTTTGCAGACACCCTAGTCCAAGCCACGCTGGTTGTCCAATACCTTCAAATATGTTTTCTGAGAGTAGGGAGGAGCTAGGAGGGGAAGGGCATGCAAGGTCTAAGGCACTAATGAAGCCTGATCTGACCCCTCTCCTCCCCCTTCCCCACCCCCTCCCACTACTCCTGTCGTTCCCTTTGCTCTGCTCCACTCACACCAGCCTCTGGCTGTTCTTTGAACACATCAAGGTCATTCCCAGCTTAGGGCCTTTGTGCCAGTTGTTCCCTCTGCCTGGAGGGTTTTTTCCCCCAGATTGTCACTGGGATGCCTCCCTCTCAGCCTTCAGGTCTCAGCACTCAGGCCACCTCTACAGAGAGGCTGTCTCTGGCCCTCATTATCTATTCACTCGACTGCTCACTTACATTTCCTTCATTGCTTTCCCTATTGTCAGAACCAACCTCCTTTACTTATGCATTTGCTTGTTAATCATATGTCTTACCCCACTAACATGTAAGCACCCAAACGACTGAGATCATGCCTGCATTTTCCCTCTGCTGTATCCCCAGTGTCTCTAACAGTGCATGGCATGATGAATGTTGGATGGATGAATGGGATTTGTTGAATGAATTGTTCTGAGTATCGACTGTGTGCCAGGCCCTGTGCCAGTGCTTTGGACATGGAGGTCTGTGCCCTCCAGCATCTCCAGGGTGGGGTGGGGAACAGACATGTCCAGTGGAAACCTTGGAAAGATTTCGAAAGGGTAGGAAGCGTGATTGTGAAGACCATACTCCTGTTTGGGTCCGTGTGTGTGGGAGAGCTGGAATCACCCCTCTTGGGCCACTTTCTCCCTTGCAG
Seq C2 exon
AGAAAGCTTACTTCTGCCAGGATCACTTCTACTGGCGCGTGAGTTCCCAGAATGAGGTGAATCAGGTGGACTATGTGGGCTACGTGACCTTCGACCTCCTGAAGTGCCCTGAGGACTAGGGCTCCCAAGCCTGCTTCAGCACTGCAGCGGGGGCCCCCTGGGGGACCCTGCCAATAGGGAATGAGCCAGTCTGCCGGATCCCAACTAGTGGATCTGTTCTGAAGGACGAGGAGGAGGGGAGGTGGGCTGGGCCCTCTCTTCCCACCTTCCTTTCTTATTAGAATGTATTTAATAAATGTGGATTCTTTAACCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(52.2=66.7),PF0004514=Hemopexin=PU(20.0=22.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(77.5=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAAGGTGGATCCCCAGAG
R:
GAAGGTGGGAAGAGAGGGCC
Band lengths:
358-1944
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development