Special

MmuINT0077561 @ mm9

Intron Retention

Description
hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079]
Coordinates
chr5:16120710-16121428:+
Coord C1 exon
chr5:16120710-16120856
Coord A exon
chr5:16120857-16121321
Coord C2 exon
chr5:16121322-16121428
Length
465 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
ACTATATTTTGTCTTTTCAGACC
3' ss Score
10.06
Exon sequences
Seq C1 exon
AAACAAAGACTTGAAAGACTATGAAGCTTGGCTTGGCATCCACGATGTTCATGAGAGAGGCGAGGAGAAGCGCAAGCAGATCTTAAACATTTCCCAGCTGGTCTATGGTCCTGAAGGCTCAGACTTGGTTTTACTGAAGCTTGCTCG
Seq A exon
GTGAGTTTCTCAGATTTTGTGTTTTAATGGAAACTAGATTTACTAAAACGTTCAGCTGCTTTTCTTTTTCTGTTGCATGTATGTTTATTATCTTATATATTATGGATATATATATCTGGGTCCATACATATCTATATATTAGAAAGAGATGTCATATGATTTTCAAATAGCAATAAGTAAATTTGGTGCAATATTGTTACACTAAAATTGAAGCTTAATAAGCAATTTTTTTACTTCTTAGAAAAATCAAAGTAATAATTTTATACAGTGAGCATTTATTATATATAATATATGTATATATGTAACACACACATACATATATATGTGTGTGTATATATGTGTGTGTGTGTGTGTGTGTGTGTGTAAAAACCAAGTGTAATATTGCACATACATTGCATGTACATGTACGTTTCTTTAGAGTTTTACCCCTATACAGAATACTCACACTATATTTTGTCTTTTCAG
Seq C2 exon
ACCTGCAATCCTGGATAACTTTGTCAGTACAATTGATTTACCTAGTTATGGTTGTACAATCCCTGAAAAGACCACTTGCAGTATTTACGGCTGGGGCTACACTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028864-Hgf:NM_010427:16
Average complexity
IR-S
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:
PF0008921=Trypsin=FE(21.9=100)
A:
NA
C2:
PF0008921=Trypsin=FE(16.1=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTGAAAGACTATGAAGCTTGGCT
R:
ATCCAGTGTAGCCCCAGCC
Band lengths:
246-711
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types