RnoINT0093256 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161418421-161421520:+
Coord C1 exon
chr3:161418421-161418524
Coord A exon
chr3:161418525-161420502
Coord C2 exon
chr3:161420503-161421520
Length
1978 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGTCTTCTTGTTTCCTGTAGACA
3' ss Score
10.61
Exon sequences
Seq C1 exon
ATTCGACTTGAAGTCTCAGAAGGTGGATCCCCAGAGCGTTACTCGCTTGGATAACGAGTTCTCTGGCGTGCCCTGGAACTCACACAACGTCTTTCACTACCAAG
Seq A exon
GTGAGGATTGCTGAGGCTGGCTGGGGAGGGTCCCTTCATGAGAAGCCTCCCACACTGGACTCCCTCCCTTAGCGACTGTTTAGTTTCTTAGCAGGAGAGAGCAAGACCTTGGAGATTCAAGGAAATGTTCCAGATAAGAGCCCTGTAGAGAGCACCCCAAGTTCACACAGCCGGATCTAAGTCCCAGATTACTTGCATATCTTTCTCTCCAGCAGAGAACACAGCTCTCTAGAAGGCTCATTCCTTGATTAGTAAACAGTAGGCAATATAATGTGCAGGACTGCCACTAGGGATACATGGAGAGGCAAGGAAGTGCTGGCTGTCTTCGGGCAAGTCACTGCCTCTCTTGGGGCCTCGGTTTCCCCATCTGTAGAATAGAGATATCATCTGGAGTCCTGTTAGGCTGATTCTAAGGCTCAACCGTCCCAAATCTATTATTTTTCAGTCATTTCCTTTATACCCTTCCCTCCAGCCATACTAGGTATCCGATAACCTTTAAGATATTCTCCAAGCCTGGGGAGAGATAAGGAATGGAGGGCAATAGTTCTGACAGTGATCCTAAACTACTACTAACGTAGAAGAAACTCACTTGGCCCCGTCTGTATGTCCAAGTTCTTCTCTCCTCCCCATATTCTCTCTTCTCCGCCTTGGATGGCTGCTCTTTGAACAGACAGATCAAGGCCTTTGGGTCAGTCGTTCCCCCAGACCCACCTACCTAAACTGTCACCTGGCTGCCTCTCTCTCATCCTTCAGGTTCACTGCTAAGGTTACCATTTCAGAGAGCCTCTTCCTGACCCTCGTTATTTATTTAGTTCTTTTTATTTCTTCCTACATCTGGAGATGTCTGTATTTTTTTTTTTTTACTGTATTTCCTCAGTACTTGGTACATAGCTGGTGCTCAGTAATCATTTGTTGAATGAATGGATGAGTTTGTCCAATGAATGTAATTGGATAAATTGATCTGAGCTTTATTTTTTTTACACTTGATCTTAGCCAAAAGGCCGAGAAGTGATGAGCTTTTTTTTTAAAAAAAAGATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTATACTTGATCTTAGCCAAAAGGCCGAGAAGTGATGAGCTTTTTTTTTAAAAAAAAGATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTATATATAAGTACACTGTAGCTGTCTTCAGACACACCAGAAAAGGGTATCAGACCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACCAGGCCATCTCTCCTGCCCTAATCTGAGCTTTAAAATAGTAACCATTCGCTAATCTTCTGATCAGTTCACAACCTGTATGTGGAACACCTATTCCCTGGGTTTGCCAGTTCTTTGGTTATCAAGGTCTGTGCCCTCCGGCATCTCACGGCAGGCAGAAGAGATGGAAGGAAGTATCAAGTAAAAACCATAGAAAGTTAGAGAAAAGCCAGGAGGAAGTGAGTCTTAGGGTTCAATTGCTGTGAGGAGATGCCGTGACCATGGCAACTTAAGAGTTAATGTTTAAGGGAGAACATTTAATTGGGGCTGGCTTACAGAGGCTCGGTCCATTATCATCATGGTGAGGAACATGGTGGCTCACAGGCAAACATGGTGCTGGAGAGGTAGGTGAGAGTTCTACCTCAGCAGCAGGCAGCAGGATGGGACAGACACCCTGGGCTTGGCTTGAACATCTGAAATCTCAAAGCCTGCCTCCAGGGACACGGGTCCTCCAGTAAGGCCATACCCCCTTCCTCCTTCTAAGTGCCACTCCCTATGAGACTGTGGGGTCCATTTTCACTCAGACCACCACAGGGTGCTTGTAAAGATCTTGTTCCTTTCATCTGTGATAACGGAGCAGAAGAGTCAGTTTTCTTGTGTCTTCTTGTTTCCTGTAG
Seq C2 exon
ACAAGGCCTATTTCTGCCATGACAAATACTTCTGGCGTGTGAGTTTCCACAACCGGGTGAACCAGGTGGACCACGTGGCCTACGTGACCTATGACCTCCTGCAGTGCCCTTGAACTAAGGCTCCTCTTTTGCTTCAGCGGTGCAGCGCAAGCCTCTAGAGACCACCCCTGAGGGGGAGGAGCTAGTTTGCCGGATACAAACTGGTGATCTCTTCTAGAGACTAGGAAGGAGTGGAGGCGGGCAGGGCCCTCTCTGCACGCTGTCCTTTCTTGTTGGACTGTTTCTAATAAACACGGATCCCCCAACCTTTACCAGCTACTCGAACCAATCAGCTTGTCTGTAGTTGTATACACATCCAAGCCTGTGGTTGGTCAGAAGACAACTTTGTAGGGTCGGTTCTGACCTTTTGTTTTTATGGGGCATCTGGGGATTGAACTCAGCTGGCTTTTGTGACAAGTACTTCACCCGCTGCACCACCTTACCGGCCCTTTTATTTATTATGTATGTGGTCATGTTCACACACATGTATTTAACCTATAGAATGCTTACTGTGCGTCGGGCGCTGCTCCAACTGCTGTATAAATATTAAGGTATTCAGTTACTCCTACTGGAAGGTATTATGTAACCATTTCTCTCTTACATCGGAGGACACCACCGAGCTATCCACTCATCAAACATTTATTGTGAGCATCCCTAGGGAGCCAGGCTCTCTACTGGGCATTAGGGACAGAGGAATTTATTGGATGTTGGTTCTTCCTTCAAGAATCGCTCAGGGATTCTCAGTGTCCTCAAAACATGCTGAAACCGGACCCCAGACTCCACTCTGGAGAATCCAACCCACTCACAGGGGAAACAGCCCGTTTAAAGTGCATGTGTGCTAGAGAGGTAGGGTAGCCGAGATGATCCCTCAGTTGGAAGGATAACCAAGTATCTTCCTCGGACACTCTTTTTTAAATAAATGAATAAATGAATATTTGTTTATTTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:12
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=PU(12.5=13.9)
A:
NA
C2:
PF0004514=Hemopexin=PD(85.0=89.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGGAACTCACACAACGTC
R:
AGGTTGGGGGATCCGTGTTTA
Band lengths:
342-2320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]