BtaINT0043634 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038496 | CR2
Description
Bos taurus complement component (3d/Epstein Barr virus) receptor 2 (CR2), mRNA. [Source:RefSeq mRNA;Acc:NM_001198991]
Coordinates
chr16:5278358-5280378:+
Coord C1 exon
chr16:5278358-5278765
Coord A exon
chr16:5278766-5280201
Coord C2 exon
chr16:5280202-5280378
Length
1436 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
ATTATCTGCCTTTCTTTTAGATT
3' ss Score
10.53
Exon sequences
Seq C1 exon
AAATTCTTTGCCCATCACCTCCTCCTATACTCAATGGAAGACATACAGGCACCTCTTCAGTGATCTTTCGATATGGAAGCACAGTCAGTTACACTTGTGACCCAGGCCCAGAGAAAGGAGTGAACTTCATCCTCGTTGGGGAGAGAACTATCCGTTGTACCACCGATAGTCAGAAGACTGGGACCTGGAGCGGACCTGCCCCACGCTGTGAACTTTCTGTTTCTGAGCTTTTGTGTCCACCTCCTCAGATCCCAAGAGGCCAAATATCATCTGGGCAGAGAGATCAATATTCCTATAATGACACTGTGGTATTTGCTTGCATGTTTGGCTTTACCATGAAGGGTAGCAGGGCAGTCCGATGTAATGCCCAAGGCACATGGGAACCGTCAGTACCAGTCTGTGAAAAGG
Seq A exon
GTGGGTATTCCAATGTTCAGAATAAATGCTACTGATTTCTTCTTTAGAAACATTAGAGAAGGTGTTATGGACTTCAGCAGGACCTTTTCCAGCTTCCAGTCCCCTCAATTATACCAAGTATCAGTTTAGTTCAGTCACTCAATCATGTCCGACTCTTTGTGACCCCCATGGACTGCATCACATCAGGCCTCCCTGTCCATAACCAACTCCCAGAGCTTGCTCAAACTCAGGTCCATTGAGTCAGTGATGACATCCATCCATCTCATCCTCTGTCATCCCCTTCTCCTGTCTTCAATCTTTCTCAGCATCAGGGTCTTTTCCAATGAGTTAGCTGTTCACATCAGGTGGCCAAAGTATTGGAGCTTCAGCATCAGTCCTTCCAATGAACATTCAGGGCTGATTTCCTTTAGGATTGACTGGTTGGATCTCCTTGCAGTCCAATGGATTCTCAAGAATCTTCTCCAACACCACAGTCCAAAAGCATCAATTCTTTGTTGCTCAGCTTTATTTATGGTCTGACTCTTACATCCATATGTGACTACTGGAAAAACCATAGCTTTGACTATACAGACCTTTGTCGGCAAAGTAATGTCTCTGCTTTTTAATATGCTGTTTAGGTTGGTCATACGTTTTCTTTCAAGGAGCAAGTGTCTATTAATTACATGGCTGCAGTCACCATGCGCAGCAATTTTGGAGTCCAAGAAAATAAAGTCTGCCACTGTTTCCATTGTTTCCCCATCCTTGAGTTGGAATCTTCCCACCTTACAGGCAGATTCTTTACCATCTGAACCACCAGGGAAGCCCAAGAATACTGAAATGGGTAGCCCATCCCTTCTCCAGGGAATCTTCCCAACCCAGAGATCGAACCGGGTTCTCCTGCATTGCAGGTGGATTCTTTACCAGCTGAGCTTTCAGGGAAGCCCACCCTCATCAAATATAGTGAATATCAGTTATACAGAAGCCTTTTAAAACACTACCATTCATTTTGTGGAAGTATCCTTGGAGGAAAAACATTAGGGATCACTAAATTGTCCCTTTCTTTAAAGTGAAAAAAAAAAAAAAAAAAAAAAACTGGAGAAAATGTTTGCTTGTCTTAACAGTGATTTCTTAAAAGAGACTTCAGCAAAATCCCACCCTATAGATAGATCAGAATCTCCCATTAGAAGCATACAAGAGGGTTCCTTAAAACAGGAAGAGACAGCAAATGAGTTGGAGCACTCAGTTGGAATGGAAAACAATCTACAGCAGCCTAAATGCAGAAAAAAAAAGAAAAAGAAAAAGATAACCACTGACCTAAAGTTACCCAAAACTGGGCTGCAAGATTACGGCTGTACTGTACAACTGCCACCAGAATGGCATTGTAGCATTGATATCAATATCTTTGGCTCAGTTTTTTCTGTTGTTTACATAAGAAAAATTATCTGCCTTTCTTTTAG
Seq C2 exon
ATTGTCAAGCCCCTCCTAAAATCCTCAATGGGCAGAAGGAAGACAGACACAGGGTTCGCTTTGACCCTGGGACATCCATAAAATACAGCTGTGACCTTGGCTATGAGCTGGTGGGAGAAGAATCCATACATTGTACCCCTGATGGAGTGTGGATGCCCACTGCTCCCACATGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038496:ENSBTAT00000063039:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.066 A=NA C2=0.100
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=48.9),PF0008415=Sushi=WD(100=40.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCCCAGAGAAAGGAGTGAA
R:
TGTCTGTCTTCCTTCTGCCCA
Band lengths:
354-1790
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development