BtaINT0129395 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:30992122-30994882:-
Coord C1 exon
chr2:30994829-30994882
Coord A exon
chr2:30992260-30994828
Coord C2 exon
chr2:30992122-30992259
Length
2569 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TCATTTTTTATACTTTGTAGGTA
3' ss Score
9.01
Exon sequences
Seq C1 exon
GCCACATTTAAAGGATGGATGGATATCATGTATGCAGCAGTTGATTCACGAAAT
Seq A exon
GTAAGTCTATTTAGAGGAAAAACTGTTTAATTAGATCTAGTGACTATTTCTACAGTGTTGTAATTTACTGATATTGTCAATAAAATAAAACCATAGGTCAATTTATACAGAATATCTGCATTAGAAAAATAAAATATTCAACCTTACATTACTTCTTCCAGAACTTGATTTGAATGTATTTCTCTGTTCACTGTGAATATTCTAACATATCTTTCCTAGTGTCTAGAATAGCAACTGGCACTTAAAAATTTGTAGATTCTATTTGTTCTATTTGTAAATAGAGATATTTTATTTTTGGTTCTAATAGTTCTAGCCATGAATTAAAAGCCCTTATAGGCGCTCTCTTCATCTGTCTCAGATTTCCTCCAGCTTTTGATATTCTTTTGTGATAGGAAAGTCTGAATAATGATAACAGAAAAAAAACAAATATAATCATATTTCTTTTCAGAAAGTAAGATTTTATGATAAAAAGGGCTTTCATAATGTATCTTACACACATCAGCACTTTTGAAATTTTTTGTGGTAATCTCCATATAATTTCTCACTATTTAACAATGAGGAGGGAAATCATGTTTTAAAAAAGAGATTGGTTTCTCATACATTGTCAGAGCATAGTAATTAAGCTCAGATGTTATATCCCTGACACCAAAAACATGTGGTAACTTAGAGAGAGTTCCTGAATTTTTTTCACCTTATTAAAAAAAAGAAACTATAAGAGCTTGACACCCTGCATTTTATCTCTTTTATTATCAGGAGTCCCATTTATAGGCTCTTTTGAATAATATTAATAATTTATAATTTATTACCACTCACTATGTTAAAGGCTTTCTTACATTATCTCATTTTCCAAAGTAGTTTCCTACCTATTTGATTAATTCAAAGTTCTCTCCACCTTTCTAATCAATAACCTACATGACATACAAATTACTTTAGGTTTCTTCCTTAATAACTTAGCAAACACTACTGTATTTTGTTGTTCAGATGCTCAGTCATGTCTGACTCTTTGCGTCCTTATGGACTGCAGCACACCAGGCTTCCCTGTCCTTCACTATCTCCCAGAGTTTGCTCAAACTCGTGTCCATTGAGTCTGTGATGCCATCCAACCATCTCATCCTCTATTGCCCCCTTTTTCTTCTGCCTTCAATCTTTCCCAGCATCAGGGTCTTTTCCAACAAGTCGGCTGTTTGTATCAGGTGGCCAAAGTATTGGAGCTTCAGCTTCAGCATCAGTCCTTCCAATGTTGATTTCCTTTAGGATTGACTGGTTTGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAGCACCACGGTTTGAAAGCATCGGTTCTTCAGAGGTCATACTAGTATATAATCCCTCAGCATTCAAACACCTTACAAAAGATGAAATTCACTTGGCTTCTAAAAGTATGGAAAGTTATTCACCCTTACTCTTGTTTAGTCAAGAGAGAAGTGCAAATTTAAACCAAAATTAAATATTACCTACATACTTTCCTGACTGGCAATATTTAAAAGTCTGACAATATCAAGTACTGCCAAGAACTGCAAGAACTCTGGTATGCTGGGGGTGGGGTGGGGGAATGGGAAAACGGGTAAATATTCCTTTAAAAGGCTCCCTGGTGACTCAGATGGTAAAGAATCCACCTGCAGTACAGAAGACCTGAGTTCGAACCCAGGTTCAGGAAGATCTCCTGGAGAAAAGAATAGCTACCCACGCCAGTATTTTTGCCTGGAGAATTCCATGGACAGAGGGGCCTGGCAGGCTACAGTCCATGGGATTGCAAAGTGTCTGATGCAACTAAGTGACTAACATGTTCACTTTCATTTCTTTAAAAGAGTTGAGCATTATCAACATTATTCATACTTAAAAAAAAAAAAAAAACAGAACTGTGTTGGATAAGAAAGCACATCATTGTTACAGAAACAGTACTTAAGACCTGCTAAGTACAATGGATCAATAGACTCATTTTCAGAATGGAAAGATACTACTGATGTACTTATGTCAACACATATGGTAATAATTCTAGTCTAGCAAGAGAAATATATAACAGAAATCAAACCCTTACTCTTACCTATTACTATTGGCCAGGTTCTATTCTAACACTTCTCATATAGTAATATATTTAGCCTTCTGAATGACCATATTAGAGTTGGTTCTGTTTTTTTTTCCATTTTAAGGATGAAGAAACTGAGTCAGAGAGAGTAAAATTTGAAAAATTTTAACAAAAACTAGTGTAACTGTAGCATCTCTTCTGTAGGAAGAAGAAGTACTCACCCCGCATGCCCCACTGGGGTCTTAAAAGTGCATTCATATCCTAGGCATTTATTGGATGAAATGAATTTTAATTATTCAGACTTTTCTATGAGTTGTTTCATTTTCTCAAGTCAATGAAAGAGTTTGGAGACTCTTCAATAAGTGTGTTAAACTTGATCTTTCCTAAAATCTGTTTAACTTTTTAAAAATTTCCAGTGATAGAGATATGCTTTGAGAATTGAAAATTCACTGATGTCTTTTCTATGAAACAATTTTTAGGTCTAATGGTTATCATTTTTTATACTTTGTAG
Seq C2 exon
GTAGAATTACAACCCAAGTATGAAGACAATCTGTACATGTATCTGTATTTTGTCATCTTTATTATTTTTGGTTCATTCTTTACTCTAAATCTTTTCATTGGTGTCATCATAGATAACTTCAACCAGCAGAAAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:23
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:
PF0052026=Ion_trans=FE(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]