DreINT0131461 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10012793-10015786:-
Coord C1 exon
chr6:10015516-10015786
Coord A exon
chr6:10013989-10015515
Coord C2 exon
chr6:10012793-10013988
Length
1527 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TTGTGTTTCTTTTTTGATAGGCA
3' ss Score
8.08
Exon sequences
Seq C1 exon
AATAAGTTTCAAGGCCTTGTCTTTGACCTAATCACCAAACAAGCCTTCGACATAATCATTATGATCCTGATCTGCTTGAACATGGTGACCATGATGGTGGAAACCGATGACCAGACAGAGGATATGGACAATATTCTGTACTGGATAAACCTGGTTTTCATCATCCTCTTCACTGGAGAATGTGTGCTAAAGATGATCTCCCTGCGCCACTACTTCTTCACCATCGGCTGGAATGTGTTTGACTTTGTTGTGGTGATTCTATCAATTGTTG
Seq A exon
GTAAGAGATTGCTTATGACTTTTTAACATTCTAAAGATGTTGGACCACTTATGAAAACATTGCTGTATTTTGATCATTCATAACATTAAATGTTGTGGTCACATTTTCTGCTGTTTGGCAATTTTGCATATAATAAACCTTGTCATTTTGACAGGAATTCAAATGTTGATTAACAGAAGTTTTGATGGTCCCCTTTAGACATTTTATTGACTATTAATAACTTTGCAACTACGCCAACTAGCATGAGGCTGCGAGTACGCTGAATACTGATTTTTTTTCATCTGACACAGAACAGGAATTGTTTTACACATGTACCTGTAATCACGTGTACAATGCAAGTTCTGAGCCACTTCCAAATGTGGATTTTAATTGGATAAATATCAGATATCCAAATATCACACCTGTTTCTATACACACACATGCACAAACTTGGCTGTGTTGAAACATCATTTTAGACCTGTAGCAAGCATGAATGAGAAAACAGTGTCCTTAAGATACAGGCACACCAGTTAAGGTTTATAAAGGGGAATGCAACCCTGGTTCTTGAGTAGTCACCAGGGGTGGTTCCCAAAGCGTGGATCAGGAACCCCTTGTGGATCACAAGATAATGAGGGGGGTCACTAGGTGAATTCCCTAAATAAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACCATATTTTATCCAGGGGTATATTTTACTTAACTTTAATTTTGCTCACAAACATGCCTTAATAATAAACCCATAAAAAATGCAGTTTAAACATTTGCCCATAGTGGTTTGAGGCAGCTGATTGAGTCGACAGATTCTGGACTCCTATTGGTTCTTGGTTTGACAGTTGTCGTAACTGAAGCCACACTGCAGGAAAGTGTCTGAAAAGTTCTATCACTGCCAGAACTATATTTAAACATTGGTGACAATGGCAATTAATCTAATCTAAACCTAATGATCAAAAGCCACATTTTTAGCCAGTTTGAGTAAGGCCTAAAGGGGATCATTACAATAATGTGTTACCAAAGCTGCAACTGTAGGATTGAACCTGACTTCTGTGTGAGCTGTGCTTGATACTCTACATCAGGGGTCACCAATCTCAGTCCTGGAGGGCCGGTGTCCTTGCAGGGTTTAGCTCCAACTTGCCTCAACACACCTGCCTAGGTGTTTCAAGTATACCTAGTAAGACCTTGATTTGCTTGTTCAGGTGTGTTTGATTGAGGTTGGACCTAAAATCTGCAGGACAAAGGCCCTCCAGGAAAAGGTTTGGTTACCAGTGCTCTACATGATTGGCAATAAATCATTATACAAGTACAAAAACTACTGTTTAGCGTCTAGGCTGTAGTTTCTTGATAGTAATAGGTAATATTAGGAATATTTAAATAATTTTTGTTCATGTACTGTTTTTAGGTAGAATATGTCTTCACCCTAAATTGCTTGCTAATTGGACTTGTGTTTCTTTTTTGATAG
Seq C2 exon
GCATGTTCCTCTCTGAGATGATAGAGAAATATTTTGTATCGCCAACCTTATTTCGAGTCATTCGACTTGCCCGAATTGGTCGCATTCTTCGTCTTATCAAAGGAGCCAAAGGCATTCGTACTCTTCTGTTTGCCTTGATGATGTCACTTCCTGCCTTGTTCAATATTGGCCTCCTCCTCTTCCTGGTCATGTTTATCTATGCCATCTTCGGAATGTCCAACTTTGCCTATGTGAAGCGGGAAGCGGGGATTGATGACATGTTTAACTTTGAGACATTTGGGAACTCCATGCTTTGTCTGTTTCAAATCACCACTTCTGCAGGCTGGGACGGCCTCTTGGCACCTATCCTGAACAAGCAAGATCCAGATTGCGACAGCGAAATGGAGCACCCAGGGAGCTTCTACCGAGGAAACTGCGGCAACCCTTCGGTCGGAATCTTCTTCTTTGTGAGCTACATCATCATCTGCTTCTTGATTGTGGTCAATATGTACATTGCTGTGATCTTGGAGAACTTCAGTGTAGCTACAGAGGAGAGCGCCGAACCGCTTAGCGAGGACGACTTTGAAATGTTCTATGAAGTCTGGGAGCGGTTTGACCCCAATGCCACACAGTTTGTGGAGTACAACAAGCTTTCTGACTTTGCGGATGCTCTGGATCCTCCATTACGCATTGCCAAGCCAAACAAGATCCAGCTCATAGCCATGGACCTGCCCATGGTCAGTGGCGACCGCATCCACTGCCTGGACATCCTGTTCGCCTTTACCCTGAGGGTACTGGGAGAGGAGGGAGAGATGGATGCCCTGAGGGGACAGATGGAGGATCGTTTCATGGCCTCCAATCCCTCAAAAGTCTCCTACGAGCCCATCACCACAACTCTCAGGAGGAAACAGGAGGAAATGTCAGCCGTCGTCATCCAAAGGGCCTTCCGACGACACCGTATAAGACAAACAGTTAAGAAGGCCTCTGAAGCGTACCGTAAACAGCTACAGGACGGGGGTGGGCATATTCCAGAGAAAGAGGTGCTTGTCATTGGAAAGTTTCAAGAGAACTCAGCGTCAGACAAAACGGATATGACTCCTTCTTCTGCCTCTCCGCCATCTTATAACAGCGTGGCCAAGTCAGAGAAAGACAAATATGAAAAGGAGAGGCGAGAGAAGGAGGACAAAGCAAAAGATGCAAGGGACAGAAAAAAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.224
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=41.9),PF0061222=IQ=WD(100=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCGATGACCAGACAGAGGA
R:
CAGGAAGAGGAGGAGGCCAAT
Band lengths:
355-1882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]