BtaINT0143595 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006730 | SUSD2
Description
Bos taurus sushi domain containing 2 (SUSD2), mRNA. [Source:RefSeq mRNA;Acc:NM_001205675]
Coordinates
chr17:73408384-73410361:+
Coord C1 exon
chr17:73408384-73408459
Coord A exon
chr17:73408460-73410153
Coord C2 exon
chr17:73410154-73410361
Length
1694 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
CTCCACGCCCTCCACTCCAGGTG
3' ss Score
8.05
Exon sequences
Seq C1 exon
ATGAAGCCGACCCTGTTGCCCTGGGCCCTGCTGCTGCTGGCGACTGTCCCCGGCCCGGACCTCTGGCCTGCTGCAG
Seq A exon
GTATGCCGCTGCCCTGCCCTTCCGTCCCCTGTCTGCCTGCTGCAGTCAGACCCAGCGCAGAACCTCCCCGGGCTCAGACTCTTGTCCATCCGTCTGGCTGTGACCACACTGGGGTTGATGCCGTTCAGTCGCTCAGTCGTGTCTGACTCTTTGCAACCCCATGCGCGGCAGCGTGCCAGGCTTCCCCGTCCTTCAGCATCTCCTGGAGTTTGCTCAGATTCATGTCCATCCTGGGGCGTGCTAAGAAGAAGAAGAAATTCTGGGGAGCCCAGAGCCAAGGAGCTGCTGGTCGGGATTGGGGTGGGGGTGTTCTGGGCTATGCCTACTCTAAGCTAGCTGGGAGCCAGAAGGCGGGTCGCAGGCCGGGAGGGAGGTCGCCAGGGAGGGTGAGCACAGCCAAGCCCTTGGACTGAGTGAGACCCGAGCCCTGAGAGAGGAGCCCTCAGCCCCACTGGGCCCCCTGGCCAGCTGGAGGCAGGACAGTGGGTCCCTCTCAGGGTGGGCTGAGCCCGAGGAAGTCCTGGGAAAGGCCCTGGACTCCGGAGTCAGGCCCCTGACCCCCGCCGGGCCGGGCCAGGCTGGTTTTCACCCGTTCCCCAACCCCCTCCCGGCCAGCTTCCCATCCTAGGAAGCAGCGACATCCCCCTGCCGCTTATCTTACTTGGGGCTTCACTTAGCCTCCTGCCCCACCCTCAGGCCATCACAGCCTCGGTCAATAAATATTTATTGACGCTCCTGAGTGCCAGGCCCTGCACTGCGCGAGGCACGACCGCAGTGGTGGCTCAGGCCCAGGCTTGGCCCTTGACCAGCCCCGGGGTGGGGGTGGGGGGAGGCTGGGACGGGCCAGAGGGGACAGGGGCCTGCACCATCCCCCGGGCTCCACCCTCCAAGCCGCGTGGCCAGGCCAGCCCCAGTGGGTCGGCTCCCCACAGCGCCCCCCCACCAAACTGCCCTCTCCCCTCTCCTGGCCAGGCCGAGTCCTCTGCCGGAACTGTCCCCTAAAAGGAGGGGAGTACCCCTTGCCTTCTCCCCCGAGGGTGGGGCAGGCTCCTTCAGGACCTTAACCCGTGGTGGGCAAGCCTGCAATGCCCAGCAGAGAGAGGGACAAGTTCAGCCCGGCACCGGCCCCTAGTGGGCCTCCAAGGGGACTCTTCGCAGCCACATTCCCAGACCCCAGGCCGGCGAGCGGGGGGGGTCCTTCTCCAGGCTGCCGGTCCACTGATGTTTTAGGGAGTGGACGCAGCTCCCGGCCCATGTGGGGGGTGGTCAGGCACTTGTGGCCATCGAACACACCGACTTGGATGCTGAGAGCCAGTCTGCCCGGGGAGGGAGGCGGAGAAGGAAATGGCAACCCACTCCAGTACTCTCACCTGGAAAATCCCATGGACGGAGGAGCCTGGTGGGCTATACAGTCCACGCGGTTGCAAAGAGTTGGACACGACTGAGTGATTTCACATGTCCTCAGATCTCCGCCGATTCCAGCCAGTCATTCAGGCCCTCGAACTAAGAATTAACCGCCAGCACCTCCCCCACCCCGCCGCCCCCGACTCTGAGCCCTGCGGGTTTCCGCTGTGTCCCTGTGGTGGTCAGCGCCGTTCCCGGCCAGCTTTCTCCTGGGGCTACTTGTAAGGGGCTCCCGGGGAGAGCGAGGCGGGCACCCTGTGCCACATGGCCCTCCACGCCCTCCACTCCAG
Seq C2 exon
GTGCCCAGCTGAGCTGCTCCCAGCGCTGCGGAGACCAGAGCGGGCCATGTTCCTGCCACCCGACCTGCTTTGGCCTGGCCAGCTGCTGCGTGGACATCCGGGATTTCTGCCTGGAGATCTCGCCCTACTCTGGCTCCATGATGGGGGGCAAGGACTTTGTGGTCCGGCATCTCAACTGGCCCAACCCCGCTGACAGCGTGATCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006730:ENSBTAT00000029404:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0103312=Somatomedin_B=WD(100=58.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGAAGCCGACCCTGTTGC
R:
CTGCAGATCACGCTGTCAGC
Band lengths:
284-1978
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development