DreINT0131129 @ danRer10
Intron Retention
Gene
ENSDARG00000010279 | scamp2
Description
secretory carrier membrane protein 2 [Source:ZFIN;Acc:ZDB-GENE-040426-2702]
Coordinates
chr25:2897354-2899160:-
Coord C1 exon
chr25:2899032-2899160
Coord A exon
chr25:2897514-2899031
Coord C2 exon
chr25:2897354-2897513
Length
1518 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
ATGTTTGTGTGTGTGCGCAGGGG
3' ss Score
9.73
Exon sequences
Seq C1 exon
GCAAACAGAACAACTGGCCTCCCCTGCCCAAGAGATTTCCCATCCAGCCTTGCTTCTACCAGGACTTCTCAGAGGAGATCCCTCAGGAGCACCAGCGTCTCTGCAAGATGATCTACTACCTGTGGATGT
Seq A exon
GTGAGTGCGCAGGCCTCGACACACACTAACACACACACCCTTACATATACTAGCACATATCATCAGTCTTATTCTGAAAGATTCGCCCAGGCCTGTTGTTTCAGCATGAAATTATATAAGCTAAATCAAAATATATTAAACAAATATGAACTTTTCACCCTCCAGTTCATTCTCATTTTATTTTCTTGTTGAATTAAACGAGTAATAAATATAACAAGTTATTTTTGTGTTATTTACATGCTAATAAAGTTTTTATTAATTATATTTGTATTTTAGTTTTGAAGTTTTGATTTGATTGTACAATATTTCTGTTTAGCTTTATTTCATTTGCGTATTTATTTTATTGTATATTAGTTCAGCTTCTTTTAGATTTTGGTATGTTTTTAGTATAACTATAACAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACATACATACATACATACATACATGCATACATACATGCATACATACACATATATATATATATATATATACACACATATATATATATATATATATATACACACACATATATATATATATATATATATATATACACGTGTGTGTATGTATATATATATATATATATGTATATATATATATGTATGTATATATATGTGTGTATGTATGTATATATATATAATATATATATATATATACACACATACATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGAGTACCCGTGGGTCTTAAAAGCATTAAAAAAAGTTTTAATTTTGATAATCTTAAATTAAAGGCTTAATAGCCTTGAATTTGGTATACAAAGTCTTGTATTTCGTCACAAAGGTCTTATTTTATTACTTAATTTTTACCTTTCCTAGGATCAAGTTCATACTGTACCAAAATTAGCTCTTACTCATTTTGGCTTATTAAAAATTCATGCAGCGAGAGTGCACCTTGCGATCCGCGTCATAGCAGAAAGCGCGAAAGCATGCTCCCCCGTTACTATGGTTAGTAGGCAAGTGAGGTACAGAACAAGATAGTCGCTAGCCTAGTTTGTCGGCTAAAATGGGAAAGCGTCGGTTTAATCCGCTGTGGCCAAGGAATCCGAATTATGTTTGGGTCAAGGAAATGAGTGCGACGCCTACTGCTGTTGGTGCCGGAAATCTTTTAAGCTTGTGACGATGGGTGTTACGGCCCTGGAATCCCATATGAGGGGTGCCAAACACTACAACAATATATATCAATATGATAAAACAATATCGTATTGATAAAGATACTGTTTTGTTTACATGTTTAATATAGCTTAATTCCATTGTTCGGATATACATGAACGTTTCAAACACAAAAATGATACTACTAATCAAAATATTTTCATATATTATTAATAATAATAGTAATAATAATAATTCATATGTTTGTGTGTGTGCGCAG
Seq C2 exon
GGGAGTGTGTGACGCTGTTTCTGAATGTTCTGGCGTGTCTGGCTGATTTCACCACTAACTCAGAGGCAGGCGTTGACTTCGGCCTCTCCATCCTCTGGTTCATCCTCTTCGCTCCCTGCTCCTTCATCTGCTGGTTCAGGCCCGTCTATAAGGCCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000010279:ENSDART00000053405:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.125 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF041448=SCAMP=PU(23.6=95.5)
A:
NA
C2:
PF041448=SCAMP=FE(29.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAACAACTGGCCTCCCCT
R:
GCCTTATAGACGGGCCTGAAC
Band lengths:
278-1796
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]