DreINT0131454 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10066150-10070432:-
Coord C1 exon
chr6:10070110-10070432
Coord A exon
chr6:10066269-10070109
Coord C2 exon
chr6:10066150-10066268
Length
3841 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTTGCTTTTCTCTACCGCAGACC
3' ss Score
11.71
Exon sequences
Seq C1 exon
CTCCCAGAGTGACCGGAGATTAGCTGGTGCAGCTACCAGAGCAGGATGTCAATATGGCTGCTCAGCTGCTCGTTCCACCCGGACCTGACAGCTTCCGGCCCTTCCTGCCCGAGTCTCTCGCCGCTATCGAGCAACGCATCGCAGAGGAGGTGGCCCAGAGGCCCAAAGGCGAGAGACGGCCTGATGACGACGACGAAAATGGGCCCAAACCCAACAGAGATTTGGAGGCGGGAAAACCCCTGCCGTTCATCTACGGAGATGTTCCGCCACACATGCTGTCCGTCCCGCTGGAGGACCTGGACACCTACTACAGCAACCAAAAA
Seq A exon
GTATGTGACCGATCATTTTTAGAAGGGGAAAATGTCCCTGGGTGTTGTTTTTGTTTACATTTAGAATTTAGGCTGTAGGACTACCTGAAGGGAATGTACTTCTGAAAATGTTAATTCTGTCATATGTTGAACAGGAAAGAAGATATTTTGAACAATTTTGGAGACTAGTAGCCATAAGCTATGTTTATATCTCAATATGTCAATCCAAGGGGACTTTCACATCTGCCTTATTTAGTTCGGTTGAAGTGCACTAGAGTTCGTTTTTCCTTGTTTTAGTGTGGTTCGTTTGGGCAGGTGTGAATGTAGCAATTGTACTCGAGTGCGGACCAAAAAAGCATACCGAGACCTCCTTGGAACCTGAACCCTGGAGCGGTTCGTTTGTGGTGAGAACATAATCCGAACTAAAACAGACCCAACCGCAAAAAGTACTGCGCCTTTTTGGACTAATCCAGTTGATGTAGTCTAATGTGCTATGCATTATGGGATATGGAGGAAAAATATTTGTTGACAGCACTTTTCCAACAGTTTTAAACAGAGAGAGAAAGAGGAAAAAACATAAGCTGATGGATTGTTGGTAATATTTCCTGAAGATGACCATGTCGCAGTTTAGCAAAAATAATTCATGCCTCCTCCTAAAATAACGTGCGATGCACCTTCATCGTTTGCAATGCATTAAAACACTTTCCAGCTGCAGCCGCACTTCATTCTTAAAATGTATAGTTTGTCTAAAGTGATGTACACAAACTAGACAGTAGATAATATGACCAGAGATACAATTAGTCAGCGCAGTCACCCCTTTATAGTCAAAAGTGACATTTTGTCTCTGCAAGTTTGTTTACTTACGAGAGTTCCATTGGCATTTTCCCGCATGTGAATTCTGACCAATCAAAAAGCAGTTTAGGAAATACATTCAACAACATCTGGCCAATCAGTGATGTGGATTTTCTCAGATCACTGCATTTTGGTGCTTTTCAACTGGTTCGGACTAAAGCAATCAGTGTGGTGTGAAAACGACCCAAGAGACGGCAGAAAATGCTACAATGTATCATTTATTGCCTTTGGTCTGGACCAAATTAAGCGAACTACAGGTGTGAAAGTAACCTTAAATGGGTGCTCAGTCGATCAACAAAAAGTACAAAAATTATACAAAAAGGCGGCAACACCAAAGCTTCAAAAATATAAATTTATTAACGTGAAAAAGGCTATCACAAAGTGTGTGACGTTTCGAGTAAACTGGCTCTTCATCAGGCAATATTTATCACAGCGTGCTACTTTCTATAGTCCTCTGAATCATCACATGGTCTCACACGTGATCTCATGACGAAAGAAAAATAAACGTTATTGAATTGAACACGGGGGCGAAGCAGTGGCGCAGTAGGTAGTGCTGTTGCCTCACAGCAAGAAGGTCGCTAGTTCAAGCCTCGGCTGGGTCAGTTGGCATTTCTGTGTGGAGTTTGTATGTTCTCCCCGTCTTTGCGTGAAAGACATGCGGTATACTGTAGGTGAATTGGATTAGCTATTGTTTGTAGTGTATGAGTGTGAATGAGAATGTATGGATGTTTCCCAGAGATGGGTTGCATCTGCTGCATAAAACATATGCTAGATAAGTTGACGGTTCATTCAGCTGTGGCGAATGAATCCCTTTATGATTAATAAAGGGACTAAGCCGAAATTAAAAAGAATGAATGAATTGAACACAGGGTGGTGCCGTGAATCAGTGGTTAGCACTGTCACCTCACAGCAAGAATGTCACTGGTTCGAGTCCCGGCTGGGTCAGATGGCATATCTGTGTGGAGTTCTCCCTATGTTGGTGTGGGTTTCCTCCTGGTGCTCCGGTTTCCTTCACAGTCGGAACACATGCACTATAGGTGAATTGGATGTACTTAATTGGTTGTAATGTATATGTGTTTATGAGAGTGTATGGGTATTTCCCATGACTGGGTTGCAGCTGGAAGCACATCCGCTACGTAAAACATATGACCGAATAGTTGCCATTTCATTCCGCTGTGGCGACCCCTGATAAAAAAGGGACTGAGCCGAAGGAAAATGAATGAATGAATGAATTAATTAATTAACCACAACTTACATATTCATAAAGAAAATACAGAAAAACAACACAATAACACATCCTGTTTACTAAACCCTAAATAAAGAAAATAAAATAACAAAATATTGCCAAAAACCTTTATTATTATTATAATTATTATTATAACCTTTATTTTACCAGGAAAGACACATTGAGATTAAAACTCTCTGCCCAAGATTAGGCAGTACATGTCACATGGGTCTAACAAACAAAAAACAATTGAAAGTGACACTGATTCACACTGACAAACTATTCAGAACATCTACATGCCTGTGTTTCAATTTCTACATCATTTATACTTTATACTTTACTCAAACACATCTAATTAAACATTAAAGAAATGGACGAATCAAAATATTCATTGCTTAACAAACAAAATTAAATATGTAGGCTAATGGATATCTGTGCGTTCAACACCGGAATAAAGAATAAAAGCAAAGTAAAGAAAAAGTAAAGAGGTGGAAAGGAGGAGGCGCGTTCTTTATCCTCGTGCTGCAGATTGTCTGTTTAACTGTTTTCTCGATAGTGAAGCGTTACGTTTTTTCACTTACAGTCTGCCGTGTAAAAAGCAAATGCGCCATGGCGCGACGCAATTGACTCTTAAAGGGAATAAGAGATGAGACTCTGATTGGATTAAAGCATGTTATGCTCAAAACACACCCATAACTCATTAATAAAATAAGCACAACCCTGTTAGACCATGTGTCAGGGTGCAGTGTATTTATACAAGCTCTTAATGCTTTTGCGCCATGTGCTTCAGACTTTGCACCTAGATCATTAAAATATGCCCTATGCCTAAAGTGAAATATCAAAAGGCTTCACATAGTAAAAAGCTATTTATCCAGATCTGGACAATTTTTCTTATATAATAAATTACTCAGAAGACAAAAATGCATCACTATGAATGTGAACTGGCTTTTGTAGTTTGTAGTTTAATAATCTTTTTTTTTTCATTTATTTAGTAACTGTGCTTCCATCGTAGGTTATGCAAATGTTTTCTTATCAGATGAAGAGTTTATCCTACTCCATTTGTCATTTATTCATTTTCCTTTAGCTTAATCCCTTTATTCATCAGGGGTTGCCACAGTGGAATGAACTGCCAGCTATTGCAGCATATGTTTTACACAGCAAGTCTTCTTCCAGCTGCAACCCAGTACTGGAAAACACCCATACACACATTTACTAACATACTGTACATTACGGTCAATTTAATTAATTCAATTCACCTATAGCGTGTGTCTTTGGAGTGTGGGGGAAACTGGAGCACCCGGAGGAAACCCACACGAACACGAACACGAACACGAAGTCCACACAGAAATGCCAGCTGACCCAGCCGGGATTCAAACCAGCAACCTTCCTGCTGTGAGACAAAAGTTTTAACCACTGTGCCACTGTGTCATCCTTAAGTTTTTCATTCACAGTTTAAAATGTTTACGTACATCTTAGCGTTCCCATTTAGCGCTATTGTTTATGTGATATTTAAAAATGTGCAGAAAAATGGGCAGATTAAAACATAGCTACTGACTTCCATAGTATTTTCTTAACAATGTCAGTGGCTTGTAGTTTGAAAAATTCTTTCAAATATCTTCTTTTGTGCTCAACATCCAAAAAGCAACTCATTTTGAGCGTAAATATGCATGTTTAGTTGAACTATCCAGTCTGATGTCAGGACGTGTGTCATTCTCTGCAGTTATGTAACACCTTGTGAAACAGATTGTGTGCGCTGTAACCACAATTTGCTTTTCTCTACCGCAG
Seq C2 exon
ACCTTTATAGTTTTGAATCGTGGGAAGGCTATATTCCGCTTTAACGCTACGCCGGCCTTGTATATTTTGAGTCCCTTCAATCCATTAAGGAGAATCTCCATCAGGGTCCTGGTGCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.344 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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]