MmuINT0178800 @ mm9
Intron Retention
Gene
ENSMUSG00000042097 | Zfp239
Description
zinc finger protein 239 [Source:MGI Symbol;Acc:MGI:1306812]
Coordinates
chr6:117819236-117822784:+
Coord C1 exon
chr6:117819236-117819291
Coord A exon
chr6:117819292-117820273
Coord C2 exon
chr6:117820274-117822784
Length
982 bp
Sequences
Splice sites
5' ss Seq
CCGGTTGGT
5' ss Score
5.21
3' ss Seq
TTAAATTCTCTGTTTCCTAGGAG
3' ss Score
8.57
Exon sequences
Seq C1 exon
AACTCTGAAGGCATGACGGTTTGAGCTCTCGTGCCCGCAGTCTGCTTCCACAGCCG
Seq A exon
GTTGGTTGGTGTACAGTATTTTGTGTTATGTGTGTTCATAGACTTTGATGCGGTGGTACCGTTGTTGGTGTACTAATCTTTCATCCCATGCTTGTCAGGCAAAAAGATTTCCATTTTGTATCTTACAGCACTAGCAGTTGTTAAAGTCACACACCGACTAAAGGGACATTGAGCAAAAATAAAGTGAAATGCAATGTGTCGAGGTCCAAGACCCATGGTCTTTACAATAGTACAATTTTACATATATGTATATATATTTTTCAGCTCTGCTTAAAAGCAGAGAAGAAATGTCTGTCTTGTGAACACATGTTTCTCTTTTCTGACAATAACCCAAAAGATATAAATACAAGCACAAACTAAGGGCTGAGGCTATAGTACAATGCTAGAATATTTGAGTAGATCCTTGGTTCAATCCATAGCACCACAAGAAAAGGAAAAGAAAGGGCTGGAGAGATGGCTCAGTGGTTAAGAGTATTGACTGCTGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCAGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAACAAGATCTGACTCCCTCTTCTGGTGTATCTGAAGACAGCTACAGTGTACTTACATATAATAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGTATTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCACCTGTAATGGGATCTGGTGCCTTCTTCTGATCTATCCGAAGACAGCAACAGTGTAGTCATATACATAAAATAACTAAATAAAAAAGAAAGAAAAGGAAAAAGAAAGAAAGGAGGGAAGAAGAAGAGAAGAAAAGAAAGCTAAGTTCTGAGTTACCAAGTGTTCAGGCCTTAGGTACTCCTAGTATAGAATCCTTTGTTCTTATCATTAAATTCTCTGTTTCCTAG
Seq C2 exon
GAGAGTCAAACACAAATTCTGTGGAGAATCTTCAAGAGAAAGACCTTCAAGAGTCTGGAGAGATGACTCAGAAACCAAGAGCACCCCTAGCTCCTGTAAGTTCAGTCCCCAGCACCCACATGGTGGCTCACCATCCATCACTCCAGTTCTAGGAGAGCCAAGGACCTCTTTCACCTCCATCAGGACCATACTGGCATGTGCTGCACAGGCATCCTTGCAGGCAAAACACTTAACACGTGAAATAAAAATCTTTAAAGTGAGAGAAAGAGAAAAGACTTCAGGATTTTTCCTAGTGGCTGATTTTGAAAGAAATGGCCAGTCAGTAGCTGGAAGTTGAGTTTATATTGTGAATCTTCAAGAGGTACACACCAATACTGAAGTAGATTGCTGTCAAAAGTGGGGAGAAGTGTCTTGCCATATTTCCCAAAACCACAGATTTCGGTGACTCTTTAAAGTTATTTCACCAACATTGAAAGTGGAAAAAAAATTTTTTATCTTTGAAATCCTAAGCCAAATAACCAGACAGGTCTCCTCTGAAATGTGTGTGTGTGTGTGGGGGGGGGGAGTCTCTCTGCAACTGAAGAAAGAGGGAGAGAAAAGGAATAAGGGAGAGTTTCATCCCACACACCACTGTTGAGAGACTGGTCAAGTCAAGCTTCCAGGTGATGTGACAGAACTGGCACCTCCAACATTCTCTGCTGAGACAATGCGCCAAAAATGTCTCCTTTGACTGTAACAGTAAGGACATTTTTATAGGGACGTCACCATTAGTCACTTGGAGTCTTCAAAGAGAGACGACACAGAGGAATCCGGTGACTGGTGATTCCTAGGAGATGCTTATCACCAACCCAGATGGTCACCTCTTCAAGAAAATCCCCACTTCAGAACAACTGTGCACGCGTGATCGGTGTAGTGAGGATTTCATTCAGAGCTCAGAACTGATGAGTCATCAGAGAGACCACCTGAAAGAAAAAGCCTGCGGGCGGGAGCATTGTGGCAGGGCCTTCACTGGCCAATCAAGTCCCGTTTCCGCATCAGGCAGTCCACATGGCTGAGAAACCTTACAAATGCGACAAGTGCGGGAAGGGTTTCACCAGGAGCTCGAGTCTGCTTGTCCATCATTCCGTCCATACCGGTGAGAAACCTTTCAAGTGTGACAGGTGTGGGAAGGGCTTCAGCCAGAGCTCAAAGCTCCACATCCACAAGAGAGTCCACACCGGTGAGAAGCCGTATGCGTGCGAGGAGTGCGGTATGAGCTTCAGTCAGCGATCCAACCTGCACATCCACCAACGTGTCCACACCGGAGAGAGGCCCTACAAGTGTGGGGAGTGCGGAAAAGGCTTCAGCCAGAGCTCGAACCTCCACATCCACCGGTGCACCCACACGGGAGAGAAGCCGTACCAGTGTTACGAATGTGGGAAAGGCTTCAGCCAGAGTTCAGACCTTCGGATCCACCTCCGAGTACACACCGGGGAAAAGCCCTACCACTGCGGCAAGTGTGGGCAGGGCTTCAGCCAGAGCTCCAAACTCCTCATCCATCAGAGAGTCCACACGGGTGAGAAGCCGTATGAGTGCAGCAAGTGTGGCAAGGGCTTCAGCCAGAGCTCGAACCTCCACATCCACCAGCGGGTTCACCGCAAGGAGCTTCACTAAGTAACATGAGCCCACTCAGAAGACTTTTATTGTAAAGATAAATATTTTTCACGACCGAGTGTGCATATCAGAGGTAGCATGCTTGCCTAGCATGTATCAGTCCCTGAGTTTGAGCCCTGATACGCCCCCACCCACACACACACACACACGGTTTCCAGCTTATTAATACTTTGTGCATGTTAGGAATGTGTGTTCATGCAGAGAGGGGTATGTGTGTTGTGCTGGTGTGTGCATGTATGTGTGCACGCACGTGTGTGGACGTCTGAGGATATCTCAGATACTACATTCTGTATGTGAGACTAGGCATCTGTCTGTCACACATGGTGTGTAATGTCACCAAGTAAGCCAGGCCAGAGTCCCATGGATCTAACTGTCTCCACTTCCCAGCTCACCGTGGCTAGGGTTGCGGATGTGTGCCACCACATCCAACCTTTTTATGTGGATTCTGTCTCAAGCTTTCTAGACAAGAGCTTTGCTGCCTAAGCTATGTCCCAGGGCTCCAGTTTAATACTTTAAACTCTTACGTTTGAATTCCTCAAAGGAAAGAAATAGTTAAGGGTTATTCCGATATAGCCCCTCACAGAAGAAATCAATCCGAGTACTCAGCACATTTTATGTTATACAGTGAATGGGTTACTCTGGTTTCTCATATGGGTAGAGTGTATAATGCAATTCTGCCAGTGTTGTTAGAATTATATTCTACATTTTTTAACTGCAAGAACTCTGTATTTTTCCAAGCACAGCATGGTTCCCTTCATTCATATTCTCTGAGAAATTGGAATTCATGTTTCCTCTGAAATTATGTGCCTTGTTTTTCATATTCCATTTAAGTCCTAAATAGCTCTCTTTAAACTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042097-Zfp239:NM_008616:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.420
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=7.9),PF134651=zf-H2C2_2=WD(100=12.9),PF134651=zf-H2C2_2=WD(100=12.4),PF134651=zf-H2C2_2=WD(100=12.9),PF134651=zf-H2C2_2=WD(100=13.4),PF079757=C1_4=WD(100=26.2),PF134651=zf-H2C2_2=WD(100=12.9),PF134651=zf-H2C2_2=WD(100=12.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGCAGTCTGCTTCCACAG
R:
TCCAGCTACTGACTGGCCATT
Band lengths:
353-1335
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
Other AS DBs: