DreINT0132861 @ danRer10
Intron Retention
Gene
ENSDARG00000002748 | sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:ZFIN;Acc:ZDB-GENE-040426-1933]
Coordinates
chr19:414920-417174:+
Coord C1 exon
chr19:414920-414973
Coord A exon
chr19:414974-415663
Coord C2 exon
chr19:415664-417174
Length
690 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGT
5' ss Score
6.6
3' ss Seq
TGTTATGAACTTGTGTGCAGGAG
3' ss Score
6.19
Exon sequences
Seq C1 exon
ATGTGATGTCATCAGCAGGAAGTGATGTCAAATCAGCTGTGGATTCGGCCTCTG
Seq A exon
GTCAGTGTCACACACACACACACACACACACACACACACACACACACACACACAATCATCATCAGCATTACTGGAGAGTTATTGCGGTGTGTGTGGATGAGTGAAACTGAACTAATACTGACTGTATATTTACACTGAACTGTTGATAGACTTATTGATAAACGCAGTATACGAGACGTGGCCTTCAGTGTTCATTTGTCAGGCAGGTAAACAGTGCCTCAAGGAGTTAATAAAAAGTAAACACTGATCCTAAATAAAGGTCATTTAATTATAAGATAATGGAGTAATGATCTGATTTTAGTACCTTTTAGTATTCAGTAGGTCACGATTCACACTCATTAAATAATTACTGTGCATAGCTTTTATTTTACATTCTTAGGTGGTAGAAAAAACAGACGTTTCAGCACAATGCCTTACTCAGTGTGACACAATCCACTTGTATCCCACAGTCAATCACATTACGTCATTAGTTAGACGACCTCTCAATAGTTCCAACAATCTCACTTTCATTTCAATATACTGAATTAACCACACTGGAAATATTTACCTTCACCTTTACAAACTCTGAATTGTTTTGTGTAAATGCACCAAAATACACTGCCTATATTCACTGAGAAATGGAGGAACATATTCATTTTCAAAATGGGCTGTACTCAGTTATGCTCAGCACTGTTATGAACTTGTGTGCAG
Seq C2 exon
GAGTGAAGCAGCTTCCCGACGCCGACAGTCTGAGCGACGGCTATCACTTCACTCTTCTGGGCGCGTGTGTGTTGCTAGCGTTTGTGTTGGGGGCGATCGCGTCAGGTTTGCTGGTGTCGTGTTACTGCAGACAGAGCTCTCCGTCAACGCCAGAGCCTGAAGCAACACTCGCACACACACATGCACACACACTCTCGCTCAGCAGCCTCGCTAAGATCAACCTGCTGATGGACAACAAACCAGAGAAAAAGAGCGAGTCTCCATCCGCACACATCTACTCGCCCGCTAAACCTCCAGAAGAGCTGCCACCCACGCCCGACTCGACCCCAGAACTGCCAATCAAAAACATCAAAGCCATCAGCAGCCAATGGGAGAGAAGCCACACCCACAACTCCACCCTCCAGCTCATTCCGACCAATCAGAGTCATCCAATGCTTTCAGAAAATCACAGTGATGATATAAGCAGTAGCAGTCAGCGTTTTGATGCCACCCTTATGTCACCTGCTGGATTAAAGTCATACAATCGGACTTTATTACCCAAGTCGTATTACAGCTGTCTGAAAGAGCCGTCAGAATGTTCCACGCTTCAGCAGATTCCCGAACAGCCCTCCGCACAGCGCCACGTCCTCATTAAAATGGGTAACGGGATCACCAGCGCGCGCCAGCACACCTTCAACCCCAAGATGAACTCCAATACGGGGAATATTTACGAGATCCAGCGGCCGCTCGTCGCCGGCGGCTCGTGTTTGACGCGGCAGCACAGTTACAGCGAGCCGCCACAGCTCCAGCGCAGCGCTATCGTCAGACGCACCGCATCGCTAAAACCACAGATACCGCCCAAACCACTGAACATACCTGCTAAAACACTGCCCTCTGCTGGCACACACAACCACACACACAACTACTGACACACACACACACACACACACACACACACAACTACTGACCCCAAGGTCACATGACACACACAACTACTGACACACACACACATACACAAATACTGACCCCGTAGTCACGTCACACACACAATTACCTACCAGCACACACATACACAACTATTGACTCCACGGTCACAAGACGCGCACAACTACTGACTCTCTCACACACACACACACACACACACACACACACACACACAAAAATACTGACCTCGCGCTCACATTACACACACAACTATTGACCACACAGTCACATGGCATACACACACAACTATTGACCCTGTGGGACAACACTGGTCACACAACACACACATGCAACTACTGACCCCGCGATCACATGACACAAACACAACTACTGACCCTGTGTTCACATGACACACACACACAAACACACAACTGAGCCCACACACTCAGGGGTCAGAATACCAGCACATTGATGACTGCAGTGTGTAAATATAGTGTGTATATAGTGTAAATATAAGAGATGGGATGTTATTATGGTGCACACTGAATGATTATGCATTGGTGGAGGGTTATTTTTGTTAATAAATCTGGTTTCTTGCATTTGTTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.629
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGTGATGTCATCAGCAGGAAGTG
R:
AGGTTTAGCGGGCGAGTAGAT
Band lengths:
346-1036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]