DreINT0131156 @ danRer10
Intron Retention
Gene
ENSDARG00000018743 | scamp5a
Description
secretory carrier membrane protein 5a [Source:ZFIN;Acc:ZDB-GENE-030131-3188]
Coordinates
chr25:31443988-31445738:-
Coord C1 exon
chr25:31445619-31445738
Coord A exon
chr25:31444145-31445618
Coord C2 exon
chr25:31443988-31444144
Length
1474 bp
Sequences
Splice sites
5' ss Seq
TACGTATGT
5' ss Score
5.54
3' ss Seq
TATGTTTTTCACACTAATAGTGA
3' ss Score
5.04
Exon sequences
Seq C1 exon
AAAACAATTTCCCTCCTCTACCACGGTTCATTCCACTGAAGCCATGTTTTTACCAAGACTTCAACGAAATCCCAGACCAGCATCGTACAATGTGCAAACGACTGTATTACCTGTGGATAC
Seq A exon
GTATGTTCACCAATTCCCCAGCAGATTTCTGAAGTATTTTCAGTACATGTCAGAGCTTATTAGGATGTGTGCCCTAGTAGATTGTAATCATGTTGCTTTTCTGCCATTACAGTGTCAATGTTTTTACTGTAAACACTGAGAAAACACACACACACACGCACAACTTGTAGAGACAGGTTTTGTATTTTAATTTGTCAGGCTGAAAACGTGGAGTGTCATATTACTTTTGCTATTGCACACGTTTAACAACTACTACGTTTAACAAGCACTACGTTTGCTTTAGCCATGTTTACAACATTCCTCTTTTATTAGCGCACTGAATGGGAACTGTTTTGAAATGGGTCTGAGAGTTGAGGAAGTAAGTGTCTGTTAGTTTTGAGCTTAGATAGATGACTTAGCTGTTAGATTTTAGTCATTTCGTGTCACACGTGAGCAGATATGACTATTTCTTTGGAGTCAATCTAGGTCCATGTATACTTGCAAAATTACAGAAAGTATTGCAAACTAAAAATAAAGAATTGAGCAAAAAATAAATAAATTAATGCAAATTTCCAAAAATCCCAAAGCGAAAATAGATTTTTGAGAAATAAAAATGAACTTTGCAAACAAAAAAAAGGAGAAAAAAGAAAAAGAAAAAAAATCAAACAGTGCAAAAAAACAAAATATTTGCAATTAAAAAAAAAACAATATATATTTGCAAAAGATTTGTATAACATTGCCTTTACAAAAACCCTTCAGTCAATTGCAATGCTCATTTTGATTTGCTTTTCAGTCAACTGTGAGTTTGCGATGCTGTTTTCTGTTTTTTTTGCACTTCACATTTCTGCATGTTTCAATTTGTGCAAAGTGAAATGCGCAGAAACGTGAAGTGCAAAGTGAAAACAGCATCGCAAACTCACGATTGACTAAAAAACAAATCAAACTGTTTTGAAAATATGTATGTTTTGTTTTGGGGGGAGTTTAAATTTTTTTATTTATTTTATTTTTTTTGCACTGCTTGTTTTTTTTCTGCAGGTCTTTTTTGTTTGCACATTTCATTTTTAGTTTCTCAAAACTTCATTTTCCCTTTTGCAGTTTTTTATTTTTGTTTTTTAAAAATAATTTTTATTTCTCAAAAATTTATTTTAGCTTTGCGAATTTTGGAAATTTGCATCCATTTATTTATTTTTTGCTCAATTATTATTATTATTATTTTTTTTGCAAAACTTTCTTTTATTTTGCAAGTGTATATGGCCCTAGATTCACCCCATATATTTCCCTTTTCCCTGTAATGTAATCAACTTCCTCCCTTTACTGTTTATAATCATATGATATTATAATATTGTAACATTTTAATTTATGATAATGTTTTAACTAAATTTATTAATGTATTAAACGGTTTCTATTGATTTTTATTTAATTGTCTCACTGTTTAATTCAATACTTTACTAGTGCAAATGTTAGTTGACACTAATTATGTTTTTCACACTAATAG
Seq C2 exon
TGAACAGTGCCACTCTAGCAGTGAACCTGATTGGCTGTCTAGCATGGATGTGCGGAGGAGGCGGAGCAACCAATTTTGGCATGGCTATTCTGTGGCTGATCCTGTTCACCCCTTGTTCATACGTGTGCTGGTTTAGGCCCATCTACAAGGCCTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018743:ENSDART00000028338:3
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=0.000
Domain overlap (PFAM):
C1:
PF041448=SCAMP=FE(22.7=100)
A:
NA
C2:
PF041448=SCAMP=FE(29.5=100)
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:
TTTCCCTCCTCTACCACGGTT
R:
TTGAAGGCCTTGTAGATGGGC
Band lengths:
270-1744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]