BtaINT0130917 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020489 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:HGNC:10738]
Coordinates
chr7:38734993-38739793:+
Coord C1 exon
chr7:38734993-38735110
Coord A exon
chr7:38735111-38739732
Coord C2 exon
chr7:38739733-38739793
Length
4622 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTTAATTCTTTGTTTATAGGGA
3' ss Score
8.06
Exon sequences
Seq C1 exon
ATACAAAACAGTATCCGGTGTTTGTGGGCCACAAGCCAGGACGGAACACCACGCAGAGGCACAGGCTGGACATCCAAATGATCGTGATCATGAACAGAACCCTCTACATTGCTGCCAG
Seq A exon
GTGAGCCCCCTTTCCCCCGTGTTTGCCTTTGGAGCATCCAACGGGCCTAATACCTAAATGTCCACACTCTGCCTCATAGTAAAGATCCTGACATTCCCAAAGACAGTGTTACTTCATTTAAAGGCTACTTTCATTTGTCAAGCAACCATTCTTTCAAGACTTTCTGTGTCCTTTTAACTTCATGAAGTGGATTTGGATAGAAATAATTGCATATTTTGGAGTTTAAACTCAATCATATGGTTTATCTTGAACATTGTGTATATACATATATATGTATATACACACATACAGTATACACAGATATTTACTCAAGCATAGCATAAAGTGTTCTCTCCTTGATACTTGCTAAATTAAGTTGAATGTGTCAACATGTATCAAATTAAGTTGAATGTATCTGTGGGTGGGTGTATGTTAAACCTGTATTTTTGCAGATAATGTATAGTATATATTATTACTTTAGCAGAATGGCAGCAGCCACCCAGTAGAAGTTTTTGATAGGGATCTAGTTCAGAAAATACTCATCCACTGGGGAAATGTTATTCAAACAGACCATGTCTTAAGGATGAATGGCCTGGTAAGACTACTACCCAGACAGGGATCATATGGATTTAGGTTTTGTTTCAGCTCTACTCTTAACTTACCTGGACCACAACTTCTCTGGCTGTCCAGTGTCCTCTGTTAAATAAGAGACTAGAGTAGAGACTAGAGTAGAATTTCTTAATGGTGTCCCCTGGGATTCTAAAAATACATGATCCCCCATTGGGGACAGGGGTTGTGGCTTATTCAAAATATTTCTAAATAAACAGCAACAAGGAGCACTATCTTGTGGGGGTCCACTGTGGTATAACCTGGGTCTAGACTGATCGTTTTACACTGGGAAGGAGAAATAGAGATTATGTTTGTAGTACCTGTCTGGCTGTGAACACAAGTAAAGTAAATAATAACAGTGCTGGTTCCTTCAAAGCACTTAGATGTTCTGAAAATACAAGCTATACAATGTAAAGTTAAAAAACACTGGCTAGATTAAAATATCCTATGAGTACCCTACATTTTGGTCACAGGGAACAATGCCAAAGCACTTTCTAAAAATTCTACTTCACAGACACTGAGTACATACTTATTGTATGTGCTATATAAATTGAAAATATAGTTGTAAGTTCTTTATAAATGTTAATTCATTCAATCCTGGGGCAAAAAAAAAAAAAAAAAACCCTTTGAGCTAGAGCTGTTTTCATCCCCATGTATACCAGGAAGAAACCAAAGTGCACAAAGGTGGAATGACTGGGTCAGAACGACACGGGCAGGATTTGAACGGGAATAGTCTTTCTCTAGAGTCTAGGCCACTACTGTCTGTGCTCTGCAGCCTACTGAGCCATGGAAGGCCTACTTGTCCTGGTAATAACCTTCTAATAGCTTTTCCCCAAGAACAGTAGCCACTGTGGGTATTCATTAAAAACATTCCAATGAGTCCCCAGTAGCCACCTCTCTGGGAGAGTATTCAGTTCAGTTCAGTTCAGTCACTCAGTCATGTCTGACTCTTTGCGACCCCATGAATTGCAGCACACCAGGCCTCCCTGTCCATCACCAACTCCCGGAATTCACCCAAACTCATGTCCATTGAGTTGGGGATGCCATCCAGCCATCTCATCCTCTGTCATCCCCTTCTCCTCCTGCCCCCAATTCCTCCCAACATCAGGGTCTTTTCCAATGAGTCAACTCTTCGCATGCAGTGGCCAAAGTATTGGAGTTTCAGCTTCAGCATCAGTCCTTCCAATGAACACCAGGACTGATCTCCTTTAGGATGGACTGCTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTTTTCGGCACTCAGCTTTCTTCACAGTCCAACTCTCACATCCATAGTCCACTGGAAAGTATTAGCTCCCTCTTAAATACCATTTTCAGTTTCCTAAATGTAACAGGGATGGAAGATTACATTTGTACCCAGTTAGCTAAAGGCTGTTCAAAACAAATGATTAAACATTATATCTGTGAGAAATAGGCTGACTCAAGAATCTTCTATGAATTTTTCACTTTGCAAGCCAGTCTTTAGGGGAAAAGAAACATAACCAACGACCTGATGACTTTAACTTGGCTGTGAAACAGTCCAAGGGGCACCAGAGTTAGGAACAAGGTGCTGTGCAGACTTTAAAGTGACCAATATTAACACTTTGTTAAAACCAAGACTGTTTCATCCTAACTCCTGACCCCAAGAAAAGAAGAAAGGAAAGAAGGAAACAAAGGAGAAACACATTCACTTTTGTAACACTATAAGACAGACTCATCTTTGGTTAAAGGTCAAATCTTGACCTTGGTTAAAAGTCAAATCTGTAACAGCTAGTATTGACATGTTGGTTTTCACTTTGTGCAGTCACTTCCCTGGAGTACGCACCCCTGGAAAAATTCCTAAATGATTTCTGTGGTTTGCATATTTAGGGTCTCTCCTCTCTCTTAAATTTCACATATCCCAACAGAGCCCCAAGAGATCCACGTTCCCAGGCAGCCACTAACATGATTTAAAGTGAAATCCTTCCCCAGACTCAAGTCATGCCAACATAGTTCAGTGGTGCTCACTGGAGAGGGGAAGAGGAAGTCCTAGGATTGAGTCAGTTTGTGTTCAAGTAACTGAGTTCAGTAAGAGCAGCGTACAAACCCGGGATGCACACATGGTGCTGGGGAAAACCCCCTGACCCTTGATATGTGGTTTAGCATAATGCATTGTTCTGTGTGTTGGGCACTGTGATCTCTTGGAGACTGAAAAATATTGCCACTGTCCAAAGGAGATTTCATTCATAGAATTTTTATTTTTAAAAGGCTCCCCAGTTCTTCTAGACAATGGGTGTCAGCTATCAGAAGCCATGTCCCCAGCCAGAACCCAGGGACTGAGTGAAGCTTGATGAGCAACGCCCCTTTTCAGTTCTGCTTTATTATTATCCATTTTGTAAATTCTTTTTTGTTGTTTAATCTCTGAACTGCTAATTAACATAAACAGGCCATGCCAAAGGGGTGGCGGGGGGGGCGGTGGCAATCAAGAGCTTTCTGAGGAATTGCCAGTGCATATTAATCAGATGTTAATTTACAGTTCATATGTTCAGCTCCTACTTAAAGTTTTAAGGAGAGGCAGGGCCAGAAAAAATCTAGAGTCATCTCAAAGCTGATACCAAAGTAATAGGCAATTCCACTCCAATAATGAACCTGACCCACAGCACCGCCAATAAAGTCAAACAAGCAATAAAGGAATGCCATAAAACTGCCTCGGAATTAAAGGGCAGAGCAGTTCTGGCACCCCACTGGAGTCTGAAGAACTTTCCAATTCAGCAATTTACAAAACAGGCTCCTCTCTCTCTCCCTCACCACTCTTACACACACATACACACTCACACACACTCACAAGGGCAAGGGAATTTTATAGGCCAACTGCCTTACCCCCTCCTTTTACTTTCATAGGAGAAAGCCTGTTTTTATTTCTGTTTTTCACTGTTGTTCTTTCCCTAAAAGTAGTAGCAAACAGATTTCCAAAGAACTGGGGGGAAAAATGGAAGTGAATCCTGACAGCAGAATTCACTTTTTTCTTTCTCTTTTCTTTCTCTTTTCTTTCTTCCCTTCTCCCCTTTCCCTTTCTTTTAAGTAATGAGGGGCCCTGAATGTCTGCATGGGAGCCTTGAGGTCTTGCTTTAAAGCTGTGGGTAATTTTCCAGCCCCAGGACTTCCTGCATTTTAGAAAAAGTCAATGTTATTTCAAGGGAAAACGAGCTGTTTTGCTTTCCCTCACTAGCCCCCCATCTCCTCAGTTGAATGTAGCGCTTTTCTTTTCTTTCTTCTGAATTCCAGACAAAAACGCCCTTGTACTCAGCTCACACAGAAGGGGATGTTTAAATATAGCCCCACACCTGAGCTGCTCATTCTGTTTCTCGCCTTCCAAGGGGAGATTGGCAGCAAATCGTAAAGACAACCAAGTTCTCAGCAAAACAGGAAGGTGAACAGAAGCAAGAAATGTAAACTTTAGCTCAAGTACACCTTAACCTTAATTGACCATCACTGTGTGAAAAAGAGTGGCTTCTGGAAATAATTTTACCTTTATCGTCTTGCGTCTTGTCAATCAAATCATCAAAGGTAAAGCTGAAAATATGTTTTTGAAAAAATGATGGAGATAGACGTTAGCTTTTTGTTAGCTCTCTTGATGAACAACTGTAGCATGTTGAATACCAAGTGAAAGGCCATGCAAACCCATCTGTGTGCTAGTTTGGAAGCCTATTTAACTTTCAGACATCTCCCACCTAAACTACGTACGTACATACAGATGTTATTGTTACCGGATGCAAGAGACTACTGGAAAGTTTTCATAAAAGGTGGCAAGATGCCATGATTTCTCTGAAGGTGCTGAATGTGTTCCTGAAGCATCTCTTAGAAGCTGAACCCTCCCCTTCTTCTTGCCCTCGGATCTTGTTTTTAATAACATGGATGTGGATTTATCTGCCTTGAATGAGACATGGACTCATTCAGGAGAAAATGCATTGGCTTGACTCTTGCATCTAACATTCTCTTAATTCTTTGTTTATAG
Seq C2 exon
GGACCATATTTATACTGTTGATATAGACACCTCACACACAGAAGAAATTTATTGTAGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020489:ENSBTAT00000043906:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(3.9=42.5)
A:
NA
C2:
PF0140314=Sema=FE(4.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
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]