MmuINT0141295 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124487940-124493506:+
Coord C1 exon
chr2:124487940-124488107
Coord A exon
chr2:124488108-124489756
Coord C2 exon
chr2:124489757-124493506
Length
1649 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CCTTCCCGTGTCTGTTGCAGGTG
3' ss Score
13.06
Exon sequences
Seq C1 exon
ACATGGAGGTATCCTCATCTTCTGTTACCACTGTGGCAAGTAGCCCAGAAATTACATCTAAAGTGATTGATACCTGGAGACCTAAACTGACGAGCTCCCGGAAATTTGTAGTTCAAGATGACCCAAATACTTCTGATTTTACTGATACTATATCAGGTATCCCAAAGG
Seq A exon
GTAAGGCCTGGCCAGGCACTTCATCTCTGACTGCATGGAAACCTGATCCCTAGCCTGGCTCTCAGAGGTGAAACTAAAGTCGAGCAGCAGTCCCTCTGGCCACAGTGACTTTGCTCTCCTGTGGTTTTTAAGTCTGAGTACATTCCTGCCCACGACATGGCTCCTGAGACAGCCACTCAGACAATCTAATCTGTATTGGGTTCTGCTGGCAGATGCTGAGAGCCTGCTGAATATCAGAGGATTCTGAGGGTCACCCTCTCAATATCAAAGGACAAAAGCTCGCAGATGACAAATACCTGTTACCAAATATTTTTATCTGGGAGGCTATCTCAGCCCCTTCTTAGCTTCATCTGCAGATGTAATGTGGAAAGGATATGCAGGGTGACAAGTTGTCCAAATGCCACAAGTGGCAAAGGGTGGCATAGTACTTGTCTGTAATTACTACGTTCAGCCCATAATAGGTGAAGTTTAAAAGCTGTATGATCAATTTGCTTGTAAGATTTAATACTCTAGGAAAAAAAAAGTGTCTGTCCCCTCATGTGTAAGCTATGGTATCAGGTTTCCAGCCAGTTCTATGGCACTGCCTTGTCATTTATGATTTACTTCTGTTGATTTTGTTTTGTTTTGTTTGTTTTATTTATATTTTCATTGCAAACAATTTTATAATCATTATTTCTGTTTTGATTTCTTTCAGTAATACCATTTCTTTGTTCTTTTCTCTCCTGGTCTTTCACAACACCATTAAATTCCACAGCTTTGGCAACTGATTGAAAGCAACTAATATTCAAGGGCCTTATTACTCACTTAATGCCAGAGAACCTTCCCAGTCCCTCTGACTCAGTTGGCTGCATGTAGAACATGTAACAGACTTGAAGACCTCTTCGCCTAACTTTCGCTAACCAATTGTTAGATGTCTGTGGTTGCATTAAAATTTCCAATAATTACAAACTAACTCACTCTTCCCTTTCTAGGTCTAATTTAAGTATTTCTCAAATGCCTCCAGATAATTTAAGGATATTTTTAAACTAATACATAGAGAATTATTTTCTTACCCTGTCCAGTGTCCTTACATAGTAGATACTTTATGAATATTTCATCCCAAGATGAAATTTCAAAACAGAACGTGAAGACAAATGCACGAGTATACATTTGTACTTAACACTGACCAAGTTCTTGCCTTGTGCTTGTGACCAGTTATGTTTCTGTCCCAGTTAACCCAACTGTCTTAGCATAGCTATTGGAGCGTGATGTGTGTGTTTGTTAATTTGGACCTCTGCTTAACCCCAGCAGCAACTCTTTAATCCTGGTTTAAGAATTAGGTGAGCATCGTAAGGTACATGTTTCCTGAACTGTTCTAACTCGCTCTCTAGATAGAAACTTAAAATTCCTAACAACTGCGTAAGAGATGGGGTGAAAGGAGAGAGAAGTCTACACCAAGGACTTGAACAGCAAGCATACGTGTTTCTGGAAATTTAATTGTGACTTCAGGGGGCGGGGGGGTGGAATACTGTGAAAGTTTGATGTCTTCTTGCTCTCGTAAGCTAGGCATATGGAGTTTGAAGGTAGTATTGATTCAATATAAGCTATTTTATATTTAATATATTTTTTAAAAAAGCATTTTGTTCAAAGCCTTCCCGTGTCTGTTGCAG
Seq C2 exon
GTGTACGGTGGGAAGTCCAGTCTGGAGAATCCAATCAGATGGTCCACATGAATGTCCTCATCACCTGCGTGTTTGCCGCTTTTGTCTTGGGCGCGTTCATCGCAGGAGTGGCCGTGTACTGCTACCGTGACATGTTCGTTCGGAAGAACAGAAAGATCCATAAAGACGCAGAATCCGCCCAGTCGTGCACAGACTCCAGCGGAAGCTTCGCCAAGCTGAACGGCCTCTTTGACAGCCCCGTCAAGGAATACCAGCAGAACATTGATTCTCCCAAACTCTACAGCAACCTGCTGACCAGTCGGAAGGAACTGCCACCAAACACGGATACAAAGTCCATGGCCGTGGACCACAGAGGCCAGCCTCCCGAGCTGGCTGCTCTCCCCACGCCGGAATCCACACCTGTCCTCCACCAGAAGACCCTGCAGGCCATGAAGAGCCACTCTGAGAAGGCCCACAGCCACGGTGCTTCAAGGAAAGAACACCCCCAGTTTTTTCCTTCTAGTCCTCCACCCCATTCCCCATTGAGTCACGGGCATATCCCCAGTGCCATCGTTCTTCCAAACGCCACTCACGACTACAATACATCCTTCTCCAACTCGAATGCCCACAAAGCCGAAAAGAAGCTTCAGAGCATGGATCACCCTCTTACGAAGTCATCCAGTAAGCGGGAGCACCGGCGGTCTGTGGATTCCAGGAATACTCTCAATGATCTCCTGAAGCATCTAAATGACCCAAACAGTAACCCCAAAGCCATCCTGGGAGAGATCCATATGGCTCATCAAACCCTCATGCTGGACCCGGTGGGACCAATGGCTGAGGTCCCACCCAAGGTCCCTAACCGGGAGGCATCTCTATACTCCCCTCCCTCCACACTCCCCAGAAATAGTCCAACCAAGAGAGTAGATGTCCCCACCACTCCTGGGGTGCCAATGACTTCTCTGGAAAGACAAAGGGGTTATCACAAAAATTCCTCCCAGAGGCACTCTATATCTGCCGTGCCTAAAAACTTAAACTCACCAAATGGTGTTTTGTTATCTAGACAGCCGAGTATGAACCGTGGAGGCTATATGCCCACCCCAACAGGGGCGAAGGTGGACTATATTCAGGGGACACCGGTGAGTGTTCATCTGCAGCCCTCCCTCTCCAGACAGAGCAGCTATACCAGTAATGGCACCCTCCCCAGGACGGGACTAAAGAGGACACCATCCTTAAAACCTGATGTGCCACCAAAGCCTTCCTTTGTTCCGCAAACCACATCTGTCAGACCACTGAACAAGTACACGTACTAGGCCTCAAGTATGCTATTCCCGTGTGGCTTTATCCTGTCCCTGCTGTTGCGAGGAAGCTGTGAGGGTACCTTCAGATGAGATACCTGCTTGTATTTTAAGAGAAACAAGTAGCCAAAGAAACTCTGTCACTTTGGTAACACCAGAACTTGCCACATGTAGCTACTACAGCAAGGCTTCTGTGTACTTGCCGGAAACGAAGGGAGGTCCTGCTCACTCCATTTCTTTCGTTTGAAGCAGAAGGGATGTGTAGCCAGGGAAGGCTCCCTTCACCAGTGTAAAGAGCTGATACAGTACTCAGAAGACTGAACAAATACTTGAAAATGGGTTCAATGTAGACTGCCATTCTGTGTGGTCTTCCCATTAAATGTGAACATTTTAATATGTATGCATTCACCTTGCCTCTTGCACAAATGTCAAAATGGAAAGATGGGAATGTCTCAAAACAAAATGAGCTTGGAGATTACCAAGCAGTTTGCTGAAAATTCAATCTTTGACCCAAACTGTAGCAATTTTTATTTTCTGAGTGTGGCACTGTTTTGTTTTATTTTTTTGTTTTGTTTTGTTTTTCAATGCCACCAACAAACTATGTTAAGAGAGGGGCGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTACCCATTAGAATTGATTTAGGTGCCCATTGCATCTTTTGTACTATGGAGTTGTTTACAGTAAGCATGACTGAACAAGCACTAACATCCTCCTACACCGGTCCATCGTGTTCGGCTCTGATCAGGAATAGACAAGGCTTCTTTGACTGTCAAGTGATTAACATATGGTACCCGGTGTCAGAACATTTAAGCGTTCTAAATAATTTTGTGCTGCTATCCATCAGAACGTCTATTCCAGCCTTGCCAGCTTAAGAACTTAGAGAAATTAAGAGGTATCTTTGATGTATCTACCAGTATTCAATAGTAACATTTACCTGTCCACTGTGAATCAAAGCCTGGGGCACGCTACTCAACCTTAGACACACTTACAGGCTTTTATTTTGATTGTGTTATTTTATTTTCCATACAGTAAAAAATGTCCTCTCTTAACTCCTCTCACCCCCAACTCCCAAGGCAAAAGAGAAACCAAAAGTAGGACAAAAGAAAGAGACAGACAGACAGACAGACAGAACAGGAATTACAGTTGGCTTAGCAGGGAGGATCTGTAGAGCTCTCGATGATCCTTCCTCCATGTGTGTCCTGTGAGGATTTTGCTCATGAGTCATGCAGGCAGTGACAGTGAACTGTAAATACCACATGTGAGTTTACCTGGATCTGTGCATTTTGTGCCTTATTCACTCGAGTGGTAGAAGTTCCGCGGTATGTTGAGTGTTTCCACTACAGAGCATCATTTCCCATGTGCCACTTGTAAATGTTTTGCAGCCAGCACCTGAGGACTTCTTATACAGTCATAAAGCCACCTAGAGCGATTTGTTGTTGAGCAACGCCGCCCCTTCCCTCCAGGATCAGAAGCAGCACCCACCCTTGCCATGATAAACATTCCATCCCCTGCTGTTCTGATAATGTGAAGTCAGATGAGGGTTCCCAGGTTATGTGGCACCTGCGGAAACCATGTCTAGAGTCGTTTCTATGTAGCTTGGCAGAGCCCACTGATGGCTGCAGGTGTGTAGCCTACTGACAGCTTTGGTTAACCCACTGCACATCACCCAGTCATTTACCCAACTTACTCTAGAAATGTCCACAGCTAAGGAAGGCTCCTGAGCCAGTCAGGCGGAGTTCAAGTGATATCTTGGGACAGTGACCATGGTCTGCATTACTTGGGGGAGGATGGGGTACAAGACACCAGATCATTTTTATACAGGATGTAGAGTACTGATGCGGTTGATCTTTTCCTTCAAGAACATTCTTTTCTATAGAAAAATGATTCCCTGTGATCTTCTGGAAGCTCCAAAGCTGAAACCCTTCAGCTTTGCAACTAAAAATATTACAGTTTAATAATCAATTAAACCAACCAACAATAAGCACTACACATCTGCCACCAACAATGTTGTTTGCATTTACCTTACCAATATTAATCCCAGCGTGGTAACTCTGTGTGACCCCGATAACATTTTGTAACATTGTGCTGCCTTAGAGTTTGTACTGTGAGTTCTATCAGTATTTATGTTGAAATTTCTAACATGGATTCTAGTCTCTATTCTGTTAATTTAATTTTAAATGCTTTATCCATTTGTGCAAAGGTAAACACAGATTGTATCTTTTTTAATGGTACGGCATAAAAAAATAACCCTAAAGTGAAGTGGCTCTATACTGTTTTATAGAGTACTTTAACGTGTATAGATATCTTGTAAACTTGTATTGTGGATGTGTAAATAATATGTACTTTGGGTTTTTAACACCGCATGTAAAGTCAAAATAAAATATCCAAGTCATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199240:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.785
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(14.9=17.5)
A:
NA
C2:
PF0143720=PSI=PD(14.9=2.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAAACTGACGAGCTCCCGGAA
R:
CTGCTGGTATTCCTTGACGGG
Band lengths:
343-1992
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: