RnoINT0131924 @ rn6
Intron Retention
Gene
ENSRNOG00000013123 | Scube2
Description
signal peptide, CUB domain and EGF like domain containing 2 [Source:RGD Symbol;Acc:1563998]
Coordinates
chr1:174428699-174430171:-
Coord C1 exon
chr1:174430092-174430171
Coord A exon
chr1:174428852-174430091
Coord C2 exon
chr1:174428699-174428851
Length
1240 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AAAAATTCTGTTCTCTTCAGGAT
3' ss Score
9.27
Exon sequences
Seq C1 exon
AAGACTACCAGGAGCTCATTGAAGACATAGTCCGAGATGGCAGGCTCTATGCGTCTGAGAACCACCAGGAAATACTGAAG
Seq A exon
GTGAGCTCCTGCCTCAGCACACAGGAAGTTAGCCACGAGCTCCCCACATACGGCTTCCAGACACTGACTCTATAGGGAGCGAGGTCAGCTCCATCCTTACCGTTACTTGATTTTGTTAAATATCAGGTTTCTGTCTTTAGTATTTTATGTATATAAACTTTAGGGATATATATTATATAATTTTGATCTTTTCTACCCTCTCCTCTAACTCGTGCCAGACCCTGAACCAGGTCTCCATAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCTCTTCCTAATAACCCACTGAGTTTAATTAGTTCAGTCATAGTATCTATGATTAGTGTACGTACATAGCTGTAGGGCCAGCCACAGGAGCGTGGGCCATGTCTCTGAAGAAAACTCACTCTCTCTCCTCCAGCAGCCATCGACTGCCAAGAGCTTCTCAGTTAAGGGTGAGGCGTCGTGAGCCTTTTACCCACACATCCTGGAACTTTGGCTTGATCTTGTACTGGTCTAATGCAGGCAAACACAGATGCATGGGGCTCATGCATGCACGTGTGTGTGTGTGTGTGTGTGTGTAGGGTGATTGCTTAGAAATCCAAGCCAGGGGAGCTGGAAAGACGGCTGGGCAGTTAGGAACACTGACTGCTCTTCCAAAGGACCCAGGTTCAAAATCCCAGCACCCACATGGCAACTCACAACTGTGTACAGCTCAGTTCCCGGGGATGTGACCCCCTCAGACAGACACACGGAGGCAGAACACAACACCAATGTAAATTAACAAAGAAAAGAAATACAAGCCAGGGGCATATAGCGTTTCTATGTTCACTTTTAATAGTGAAAGACCTTTCGTTCCTAGTTCGTGCTTCCGGCTCAAGGCTTACCACACTTCAGAGACTCGCACCTGATCGATAGTAAATACTGGGCACACCACTAATCCCAAACCATTTCCCGAATCTCTATGTTGTATCTCATCTGGGTGAGAAAAAACCCAGTTTTTATATATCAACTCCTCTTTCATGGTGCAATGTGTGCTTATTATTAGCAATTAAGAAAAATTAAAACTGGAAAGAAGATAACAATCAGAGGAAACAATTTTCACCAAGTGATTTCTAGCTAGTGAACCTCCCATCGATGTGAGTCATTATGATTCCATTGGCAAAATGTCAGAAGGTTTGAATGTTCTGGCCTGGTAACAAAAATTCTGTTCTCTTCAG
Seq C2 exon
GATAAGAAACTGATCAAGGCTCTGTTTGATGTCCTGGCACATCCCCAGAACTATTTCAAGTACACAGCCCAGGAGTCCCGGGAGATGTTTCCAAGATCTTTCATCCGATTGCTACGTTCCAAAGTGTCAAGGTTTCTGAGGCCTTACAAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013123:ENSRNOT00000052377:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
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:
AGACTACCAGGAGCTCATTGA
R:
TCATTTGTAAGGCCTCAGAAACCT
Band lengths:
232-1472
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]