GgaINT0006901 @ galGal4
Intron Retention
Gene
ENSGALG00000003392 | SBNO1
Description
protein strawberry notch homolog 1 [Source:RefSeq peptide;Acc:NP_001026640]
Coordinates
chr15:5004132-5006446:+
Coord C1 exon
chr15:5004132-5004441
Coord A exon
chr15:5004442-5006345
Coord C2 exon
chr15:5006346-5006446
Length
1904 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
TTTCTGTTCTTTTTTGGTAGCTG
3' ss Score
8.04
Exon sequences
Seq C1 exon
CAACCACCGTCCACCACAACCTTTGTGCTGAATCAAATAAATCAGCTTCCAACGTTGGGGACTACAATAGTGATGACAAAAACAACACCAGTTACAACTACGAGGCAGACTATTACTGTAGCAAAAATCATTCAGACCAGCACAACTACTCGACCCTCGGTTGCAGCACCAGCAGTACGGAATGCCTTGACCACTGCACCTTCAAAGGACCAGATCCAGCTGAAAGATCTGCTGAAGAATAATAGTCTTAATGAACTAATGAAATTGAAGCCACCTCCTAATATTGCGCAACCAGTAGCAACAGCAGCGA
Seq A exon
GTGAGTGTTCTTTTTTCATAACAAGATTTCAGATAAATGGTGAAACGTGAAGATACTTGCAGACCTATTCTCATTCATTTTTAGAGTATCAAAATAAAATGAAGTGTCCAGAAAACCTTGTAAATGCTATTCGAACTCTATTATTGATAGAATTCAGGGTGAAAGTAACGGAAGATATCAGGCTTAGAAAAATCAAGCCTGTAGTTTACCATAAGGAATGAGGAAAATGACATTTTAGAGTGCAGCTGGCATATTGGTAAAATTAATTCATGAACTTCTCTGAAGTTGATAATTTAGCTATCTTGAGCCTGCATGAGTTCTTGTTTTAAATTCTTGCTGTGGAACTATGGCAGAAGAGTACATTTTGTCTTATGAAAGAGATTTATACTATTTGCTGTTACTCTTATTACAGAGTGTTTCTCTAAAATATCTTCTAAGAAAGGAAAGTCTTTATCCCTGTATATTTCACAGGAAGCATCAAACCTGTTGTGTATAAAAGCTTGATGTGCTAAAAACCTGCTGCTTGCTTTTCATGTAACTGCTTTTAAGATGTTGCTGATTTGATAACTGTTGATAGTCTTGTGTGTTATTTCTAATCTGTGGATGGCATACATGGTCATCTTAAATGCAGAAAACTACATGTATTCTTAAATTGCAATTTGATGTTAGACTTGCATGAAACCGATATGATTTTTTTCAAGTTATTCTGATTTTAATAAGAGATGAGATTACACTACTTGAATTTGCTTGAAAAGATCTCGCTGCTTTTTCTGAGAGGTACACAGGCTTCTTACTGTATCCTCATCTCTGAAATAAGGTTTACTGCTTTTTTTATAGCAGAGTTGGAAGTAACATGTTCTTTCACAGGAGAAGGAGAAATGCTTTATAGGATTTCTGATGTAGCCCTCTGCTAAATGAAAGCTCCAAGAAGAATTTAAGTAATTATTAAGGCCCAGTAGGTGTTGCAGCAGCACAGCTATAAGAACAGGAAACAGTTCAGTATGTTTCTTTGTTAAGTGAAAAGGAAACATGCAATGTCTAGAACTGCATTTCTAATCCTGTTTGTGTGCTTGTGTTTCAGGATACTTTTTCGTGGTTACTCAAATAAAAATAGACAAATACCTTTAGGAAATTCAGTGGCAGAGAATTGTGTGGAAGGAAATGCAGTCTCCTCATGTAGTCCAGGCAACTGAAGTTCTGGACTGAAAACATGAACATAAATTATGCAGCCTCTTTAAGGCAAACACTTTATTTGTGCAATTGTCTTAGTTGTTTTCTAGGATCATTTGCACTAAACACATACACTGACTTATCAACCTAATGAAAGCTTGACAGCTCCTTTAAATGTTTTATGCCTACCAAGCCCTGTTGCTGGTTGCTCCCAAATGTGGGTGAGGACAGGCAAGATAACAGGATCCTTCAAGATGGAGACTTTCTGTAAACTCTGAACAATTGAGACCAAAGTTGATTTTCTTTTTTTCAGAAATAATTGTAGTTCCACCTAAGGTGGTAAATGCCACCAGACCAGGTAAGTTCATTTCTGTTGAAACATTGGACTTTCTGGTTTGTTGTTAAACTCCAAAGATTCACAGTGTGGAGTACTTCTGAATATTATGCCTACATTTGGTGAAGGTCTTTTTTTTTATTTTGACACTAATACACACCTGTCAGATGTGGTATTGCATGGGAAGTTTCTTTAAGTAGCAGTAGGATTTAACTCCTTGTGTGCTCAGGGGCATTTTTAGTTCTGACAAAAACATTACTTGTATTTTGAAGCATCTGTTTCCTACTGGACAGTAGCATCCTTCTCTATTAATGAGTGAGAGGAGAGGTTTTGCAATCTGACTCAAAACATTTGGAGGGTATTTTGGTTGAACACAGCTGTTTCTGTTCTTTTTTGGTAG
Seq C2 exon
CTGATCTAAGCAATGGTGCGGTGAAGAAGGAGGCTTCCACAAAAGAGGTAGCAAGAATATGGATAAACGATGTCAAAATGAGAAGTTTTTCACCTACTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003392:ENSGALT00000005363:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.529 A=NA C2=0.353
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCGTCCACCACAACCTTTG
R:
GTGGAAGCCTCCTTCTTCACC
Band lengths:
346-2250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]