DreINT0106116 @ danRer10
Intron Retention
Gene
ENSDARG00000052695 | nr2f1a
Description
nuclear receptor subfamily 2, group F, member 1a [Source:ZFIN;Acc:ZDB-GENE-980526-115]
Coordinates
chr5:49093202-49096229:+
Coord C1 exon
chr5:49093202-49094405
Coord A exon
chr5:49094406-49095701
Coord C2 exon
chr5:49095702-49096229
Length
1296 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAT
5' ss Score
6.38
3' ss Seq
CCTTTCTTTCTTTTTGTCAGCGG
3' ss Score
7.63
Exon sequences
Seq C1 exon
GGCTCCTTGACACGAGCACCATATAAGGCGCAGCGATCTCCATAGAAACGTGTCAGTTTCAATAGTAGTGTCAAAGTTCACTATATACAGACATTCGCGCAGATCTCCGTTTCGGAAACATTGCTCCGCTGGTACTCCCGTTAAAACGCATTCTTTTTGGGTCTCTGCTTCTTACATATTCCATTAGTTGCTTTTTTTCTTTTCTTTTCCTACTGGAGAGGTGAAACTACATAGCCAGTCGGGCGACGTTGCTTTTTTTCGCTGGACCAGATGAGCTTTATTCATGAACATAGATAGAGAAATCCGTTCTTCAGTGTTTCCTCCTCTCCAACCGCGAAGACGGAGAGAGGAGCAAGGAAGAAAAAAGAGGGGAATTTATTTTGCACAGCACTTTGGATCTGCGGTCCACCAGAAAGCTATTATTTTTGCTTCAACGTGAAGATTTTGTTTTTTACTGCGGTATTTTTTAAGAAAACTGTTTTTTTTTATATTACGTCTGGGATCGCTTTCTTCATTCACGATTGGGTTCCCGAATGGCTGACTGCAATTTACCTTGGAACTGGCCTCCCGACAACTGCATATCCTGATCGGGTGCCTTTCTATCGACTCCGGTATTTTGAATGTATTGACCATTTTCTGCTTCTACTTTTTTCCCTATGAGATTGAGTGCTCCGATTTGAATTCGCGCTGCCGTTCGTCCAAGACTTCCCTTTTCCCTGCTCCGATATCCGAGCGACCAGTTCGCTTGAAAGCACTTTTCGGGCCCGAGATATGGCAATGGTAGTTAGCGTCTGGCGAGATCCGCAGGAAGACGTGGCTGGAGGACCTCCGAGCGGCCCCAATCCAGCAGCTCAGCCGGCGAGGGAGCAACAGCAGGCGGCGTCAGCGGCACCACACACTCCGCAGACCCCCAGTCAGCCAGGACCTCCGTCCACACCAGGGACGGCTGGCGACAAGGGCAGCCAGAATTCTGGACAGAGTCAACAGCATATAGAATGTGTTGTTTGCGGGGACAAATCAAGCGGCAAGCACTATGGTCAATTCACCTGCGAAGGATGCAAAAGTTTCTTCAAGAGGAGTGTCCGAAGGAACTTAACATATACATGTCGTGCCAACAGGAACTGTCCTATTGACCAACACCATCGTAATCAGTGCCAATATTGTCGGCTGAAGAAGTGTTTAAAAGTGGGCATGCGGCGGGAAG
Seq A exon
GTGAATATATTTTTCTGAATACATCACACTTGCTACACAAACAGGTTTATTGTTTAAAGCAAGGTTATGCAGACCTCGCAATATTAATATGCAAACGCAAAATACTATCGTATTGAATTATTGCTAAAGAGTGTCAGAGGGCGCGTTTGTAAATACACGCGTATATATGCAAGATCAGCATGGATCTATTATAGTTTTTTTTACATAGATTGGCAAATATCGTATGCACCAATTTCAACTCGCAAATAACAATATATATTATAAAGTCACCCAGTAAACACTGTGTGTGTCAAAAAGAAAGATAAAGATTAAGTGTGTAGCTAAGCCTACGTGCTTTTACGTGTGTGCTGAAAGACGAAAAAGCTAACTACGTTCACATGCACATATAGTGTACCCTATTGAAATAAGAAGCTATAGCCTATGTTTATCTCTCGAAGTAAGATGTACAAGTCTGTTTTCACGCCGTAGCCTAGAGTAAACGTTCAGAGAGGCCTGTCTGTCCCCTCTCAGCCTAAGCTGTATGTGAACAATGGCCTTTACAACTTACACTCTAGTCTTAATAACGAGTAGTGCGAAACTGCTATTGATAATATTTAGATTCTTTTAAAAACTTAACACGTGCCCTTTGTCCTGTTTATTTTTATTCATTTATTTTTTACTTGAATTTAATAATGAAAACAAACTCTTCGTACTCGTTTGTGGACATTTTCACTGTTCCAGAGTTAGTACTCATTATTAAATTGCCTGGAAACGTGTTACTACACGTAAACCTACACATACGTATATTACAAGTATTACATATAATATTATTACAGTATAGCATTTATAATCAGACAGATGTCAGTGGCAGTGAACTAATTCTACTGAAGTCGAGATTTAAACCCGTTTTGTCCACTGTAATGTTTGCTACATGCCTATAAAACTACAAAATAACATTTCAAACGAATTTTCATGTGCGTGCGCGTGTTTGTGGAGACATAAATAGACACAAACACAGCGAGTGAGAGAGAGATAGCTAGCGTTTGTATGTCTCCATATTCTGTCCATATACAAAGGTAAACATTTACCATCCAATAATAAATGAGGTTAGTAGGGATACAAGGACCATGTGAAAAGATTTTTCTTCGAAACGCAATGCCTCACAAATAAATATTAAATATTGTGCAATTTTGTTGCAATTTCGTATATGATAAACAGCAGTCTAGACTGCTCATGCACTCGAAGTAAAGCTTCCACATCAATGATGTTTCTCAGTTCTGGATGTACATTTCCTCTCCCTTTCTTTCTTTTTGTCAG
Seq C2 exon
CGGTTCAGCGAGGAAGAATGCCTCCAACCCAACCGAACCCGGGCCAGTATGCGCTAACGAATGGGGATCCTCTGAACGGTCATTGCTATCTCTCCGGATACATCTCGTTACTACTTCGGGCCGAGCCTTATCCTACGTCTCGCTATGGCAGCCAGTGCATGCAGCCCAATAATATTATGGGGATCGAGAACATCTGTGAGCTTGCAGCTCGTCTGCTCTTCAGTGCAGTGGAATGGGCAAGGAACATCCCTTTCTTTCCCGATCTGCAGATCACCGACCAGGTGTCATTGCTCAGACTGACATGGAGCGAGTTATTTGTGCTAAACGCGGCTCAGTGTTCCATGCCCCTACATGTGGCCCCACTGCTCGCCGCTGCCGGCCTGCACGCCTCGCCCATGTCGGCGGATCGCGTCGTGGCCTTCATGGATCACATTCGTATCTTCCAGGAGCAGGTCGAGAAGCTCAAAGCACTGCACGTCGATTCTGCTGAATACAGCTGCATTAAGGCAATAGTGCTCTTCACGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052695:ENSDART00000133384:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.096
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=WD(100=48.3)
A:
NA
C2:
PF0010425=Hormone_recep=PU(67.3=74.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTGCGGGGACAAATCAAGC
R:
TGCCATAGCGAGACGTAGGAT
Band lengths:
352-1648
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]