RnoINT0131062 @ rn6
Intron Retention
Gene
ENSRNOG00000002104 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:RGD Symbol;Acc:727896]
Coordinates
chr11:30388587-30390750:-
Coord C1 exon
chr11:30390637-30390750
Coord A exon
chr11:30388744-30390636
Coord C2 exon
chr11:30388587-30388743
Length
1893 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TGTATTTTCACCGATTGTAGATT
3' ss Score
6.57
Exon sequences
Seq C1 exon
ATGATTCCTCCCAGGGGCTGCGCCTACATAGTTATGGTTCATAGGCAAGACGCATACCGTGCCCTGCAGAAACTGAGCCGAGGAAACTATAAAGTGAACCAGAAATCCATAAAG
Seq A exon
GTACATTTTTATCATTTATAAAAGGGTTTCACGTGTAAATATATTGTTGTTGGAGGTTTTCTTTCAATTGTAATTTTCTGCTTGGGAATGGCTTAAGTCATAAAAGCTACCTCCTAAACCACAGTATCACAGCTAGAACAAAACGTTACCTTAATGTTAACCAACATAAAAGTTTATGTAACAATTTTCTTAGATTCTTAGTGTTTTAATGTAGTGTATTCTTATCAAGCTTTTCTTCTCCCCCAGCTTCTTCCAGATTCCACCTCCCGAATCTCCATGGCCCCCCCTACCACACCACACCCCTGGTCTGGAAAACAAGCAATAAAATGAGATTGGGAAAAGCACAGAAAACATTACACCCTCCTGAAAATCAGAAACCCAAACACACAAGCAAAAAGTCACTAAGACAAAAATGCCCAAAGCAGCTAGAGATAAAAAGTCTACCCTCACCCCCTAGAAAAAGAGTTTGTTTTGAAGTCAGCCATGCACTACTGGGATGGGTCCTCCTCTGAGGGTAATAAACACAGTGAGGCTCCTTTGGAAAAACTAATGCTTCTTTTGCAAGCAGATGTCAGTTTCAGTAACTTCTTAGTTAGAGGCAGGAGCCTGGCTTCTACTTCTTCGAGCTGGTACCCTATCTGGCTTGAACCTGTGCAGGACATGCTGCCATGTCTGATTTCATAGGTGCATCAGTACAACAGTTGGAGTTACCCAGGCCCCGCTGGCTCTAAATTTTTTCCACCTTCTCTTCCACATAGTTCCTTGAACCCTGAGGGGAGGGTTTAATGAAGGTAGCCCATTTAGGATGCTGGTCTTTTATTTCCTATCAATTCCCCCCCCCCCCAAAAAAAAAAATCCTTCTCTGGAGATGGCTAGGGCAGGAGTTGGTCTGTGGGTATAGCAGAATGTCATTAGGAGTCAGTTTATTGCTAAGCTAACGAGCTTTCTTGTTTTGAGACAGGGTTACTTTGTGTAGCCCTGGGTATCCTGGAACTTGGTCTGTAGACAAGGCTGCTTATTTCTGCTTCCTCTGAGTGTTGGGATTAAAGATGTGTACTAACAATACCTAGCTAACATAAAAATCTAATTGATACGATTTATTTTTTTAATAAAGTAGTGGGAATTTAACCAGGGCTCTTAATGTATACTAGGTAACCCTTATACCTCCAGCCACCTTATTTATTTATGTACTTAACTTACCAGGCTGGCTTTGAACTCCTGATCTTCCTCCATCTTCCTCCTGAGTCCTGGAATTGCAGCATACAGTGCCTCGTCTGTCTAGCTATAATTGGTGCTTTAAGGATCCCCCCCCGCCCCCCCGGAGCTGGGGACCGAATCCAGGGCCTCGAGCTTGCTAGGCAAAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCCTAAGGATATTTTCTAATAAAATATTTTCTTATATAAAAATGTAGATATTTCACAACTTAAGGTTTACCACCCCTTTTTAGAATTAACTCTGAAAAAAACCAAAACCCAACAAAAGTAAAGAATATTAGAAGCGCATGGACAGCTGCCCTCTGAGGAGTCAGATTCAGTGCTGCTGCAATTACTTCCTGGTTCTACTCTAATGTAGACTGAAAAAAGATGTTGCCCTCTCTGTAGACTCTGAAAATCGGTGTCCAGTGTGTTGGGCTTCTCCCTGATAACTCGATCTTTCTCCACTATGTGCTGGCTGTGAGGAATGTATAGAGATTTTTATCCTGAGACAGAATGGGAAGATAGCAGAACCATTCATCTGATTCGCAAAGAGAAGCTTAATGTCCAGGGACAGTGAGTCCAGGCTGCTCCAGTAGAATGATGGAGAGTAGCAGACTGAAGGTTTATGACTTTGTTTCCTTTCTTTGTGTATTTTCACCGATTGTAG
Seq C2 exon
ATTGCCTGGGCCTTAAACAAAGGAATAAAGGCGGATTTTAAACAGTATTGGGATGTTGAACTTGGTGTTACTTACATTCCATGGGACAAAGTCAAAGCTGAGGAGCTGGAGAGTTTCTGTGAAGGAGGCATGTTGGACAGTGACACACTTAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002104:ENSRNOT00000002881:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.151
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(55.2=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGATTCCTCCCAGGGGCTG
R:
TGGGTTAAGTGTGTCACTGTCC
Band lengths:
270-2163
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]