DreINT0131054 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25744637-25746672:-
Coord C1 exon
chr10:25746488-25746672
Coord A exon
chr10:25744738-25746487
Coord C2 exon
chr10:25744637-25744737
Length
1750 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
TAGTTGTTCCTCTCTTTCAGTGT
3' ss Score
9.19
Exon sequences
Seq C1 exon
GTCTCCTAAAAGAAGAAGGTCTCGATCCAATTCCCGGTCCAGACGAATGAGGCATCGACGATCTCGGTCTCGAGAACGGCGGCGTCAGTCACCTCGCTCGCGCTCTCAGGAAAGGAGAGACAGAGAAAAGGAAAGAGAACGAAGACAGAAAGGCCTCCCTCCTGTTAAAAATAACACACTCAGTG
Seq A exon
GTAAGAAGGCCACTTTCACTTCTAAGTATACATAACACACTACTGAACCTTAGGTGTGGGTGATTCATCAAAATAAAATTGCAAACACATTTATGCAAAGCTGCGATTGTCATGCACATCCGGGAAGCATGGTTCTGTGAAATCTCAGATGATGGATAGAGGGCGCTCTTGTGTGGAAACTCCAAAAAAACAGCAAAGAAGAGACTAGGGTTTGGATGATTGATGCTGCTCTTAATTCAGAATGGCTCATCCCTATGCTCTAATCACTTCAAAGTGTTAACCCTTTAAAGTGACTGCTTCAAAGGGATGAAGGGTGCAGTGGTCAAAAAATAATTTTTTGGAACGCATTTTTGCGTCGTCATAACGAGACAATCGAGGAGGTGTTTTTGTCGCACATTTTGTCTGCTGGTTTACACCCACAAAACTGTAATATTATGAAATCTGGAAAAATGAGTAGATTGTGCAGGCTGCGACTTGTTTATTTAATTTTTATTATTTATGCATGTATGTTTTAACCTATACATCATTGTAATAGAATTTATAATCATTTTATTTATAACTTTATTTATAAATATCACAGCAGTTGCCAAAAGTCAAACAGCTATCTGTCTGTGTGACATCTAACAATGAATATGTCATGGGTGCCTGAGGTGTCCATCAATTGTACCCTTCAAATCCTTCATTCCAAAAGGCCCTTCAAACTAGCCAGTTTTGAGCACTTGGGTTTGGAACAACATTTCAATATGGCGGTCATGTTTCTTTTCATTTCAAAGTGCCCTTTGGAGGGCGATACATGTTGTTATTCATGGATCAATGCTTAGATTTTCGGGGTGCATAATGATTATATCTTGAGTCAAACAACAAATGGGGCTCTAGGCTAGTTTTTAATCGTATGCTTTAAGTGAGCAAGTGCTTTCGATCATTTACTGTAAGTCAGGGGTGTCCAAACTCGGTCCTGGAGGGCCGGTGTCCTGCAGATTTTAGCTCCAACTTTCTTCAACACACCTGCATAGATGTTTTTAGACTGCCTAGTAAGAGCTTGATTAGCTAGGTCAGCTGTGTCTGATTGGGGTTGGAACTAAACTTTGTAAGACACCGGCCCTCCAGGACCAAGTCTGGACATCCCTGCTGTAAGTGGTCAATTGAACTTAATTTTTATTGAATCATTCTCTTTATTAATGATTCTTTTTCATTCAAGTGGAATGAGTAGGGATTGGGAGAGTGTGGCTGTTTATAAAGCATACAGCGCCTCTGGTGTTAAAAAGTGAACTCCAAATCGATTCAAGAGAGAATCAGGATGCATTCAGAAAATCATTTCTCAATTTGCAATCAATTAAAAACCCTGCTGTAGGAAAAACCCAGGAAATCAACATAGTAATTTCCTAATAAGCTGAAGATTTCACTGCTGTCACTGATTCAGTCAAGCGAGCTTAGAGTAAAAACATGTTGATGTGGTGTTTTCACATGCTTTCAGATGGAGCAGCATTTATTACACAGAATTGCACAGAGCTGTAGTAAATTCAGACATTTGTCATTATTACAAAATGATCTTCATTTTATTATCAACCAGTTAAGGTGACTGACTTTGAGTTTGCATAGCTTGTCAACGTACTACAAACCTGTGTAGTAAATTCTGCTCCATCTGAAAGCACATGCTGGAGATTTACTTGACAAAATGTGGATAGAAATCACCTTTGACCCTATTGAACCTTTTTCCTGTTTTCAATGAATAGTTGTTCCTCTCTTTCAG
Seq C2 exon
TGTGCAGCACAACTCTATGGGTGGGTCAGCTGGATAAGAGGACACAGCAGCAGGACGTGGCCTCTATACTAGAGGAGTTTGGCCAGATAGATTCAATTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.921 A=NA C2=0.059
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0007617=RRM_1=PU(41.8=82.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCTAAAAGAAGAAGGTCTCGA
R:
ATTAATTGAATCTATCTGGCCAAACT
Band lengths:
286-2036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]