BtaINT0043642 @ 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
chr16:5286932-5288715:+
Coord C1 exon
chr16:5286932-5287014
Coord A exon
chr16:5287015-5288322
Coord C2 exon
chr16:5288323-5288715
Length
1308 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TTTCCTGTTCTCTTCTGCAGTTA
3' ss Score
11.29
Exon sequences
Seq C1 exon
GTACCGGATGATGAAATATGCTTTTCAAAAATGTCAAGATGATGAAAATAGGGTTTGGTTCCAAAGGATTCCAGTTTGTGAAA
Seq A exon
GTAAGTTAAAAAAAAAAAAAAAAGTCCATGGGGTTGTAGAGAGGTAAAGAGGATAGGTCACTGCAGAGCTATTCTATGCCTCAGCAGTGTATGTGTTCTAGCTTAGTTTATATAAAACATGTTTTGGTATTTAGATAGTACTGGCAGTGGGAAACAAAACTGTCAAGTAGGAAATGAATACCGTTGACCCTCTGTATTTGCAGGCTTCATAACTTTGTGTCAACCAACTGTAAATAATATATATATTATATATTATTTACATTTACATTATTTATATTTATATTATTTATATTATATATATTTTTAAATCCTGAAAGTTTCCAAAAGCTAAACTTGAATTTGTTATGCACTGCGTACTATTTACTTAGCATTTACATTGTATTTGTAAATATTTAGATAGCATTTATGTTGTATTCAGTATTATAAGTCATCTAGAGGTGATTTAAAATATATAGGAGTCTGTGCATAAGTTAAATGCAAACACTATGCCATTTTATATAAGAAGCTTAAGCCTCCTTGGAATTTGGTACTGATGGGGGACCCTGGAATCAGTCCCTTGTGGGTACTGAGGAATGACTGTATTTGCAGTAAGCCTGCTAATTGCTAAAAATTAAAAAAATAACAATATAAACTATTTATTTCATGGGAACATAGCTGTATTTATTCCTTTGTCTATATTTATACTCTATTTTCTGAATTATTTTGGAATGAGTATGTATTATTCATAGAGTCAAAAAATTCAATGAAGTTTTTTAAAGAAATTATGATTCAGCATCTAAAATTTAAATAACTTTATGTGTGCTCAGTTACTCAGCCATGTCCAACTCTTTGCAACCTCATGGACTGTAGTCTGCCAGGCTCCTCTGTCTATGGAGTTTTCCAGGCAAGAACTAAGTGGATTGACATTTCCTCCTCCAAGAAACAACTTTATAGCTATGTGCAGTACACACAAGGCGATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGACAGAGGAGCCTGGTCGGCTGCAGTCCATGGGGTCGCTGAGGGTCGGACACGACTGAGAGACCTCACTTTCACTTTTCCTTTCATGCATTGGAGAAGGAAATGGCAACCCGCTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACAGGGGAGTCTGGTGGGCTGCTGTCTATGGGGTTGCACAGAGTCAGACATGACTGAAGCAATGCAGCAGCAGCAGTACACACAGTTGCATAGTGGCATTTGTATCTGAATGAAGACTGTCTACTATGGTGTACCAGCTGAAGCAGAATTTCCTGTTCTCTTCTGCAG
Seq C2 exon
TTATCCACTGTCAGGACCCACCGGTGATTAACAATGGGAGGTACAGAGGTGTGCTGCCAGGAGGCTTTCCATATGGAAGCGAAGTCTCTTATGAATGTGATCAAGGATTTGATCTCCTGGGAGAGAAAAGTATACGGTGCATAAGTGATTCTAAAGGACTTGTATCTTGGAGTGGACGTGCCCCGCAGTGCTTAAAATCTCCTCCTGTGACTCACTGCCCTAACCCAGAAGTCATGCATGGACACAAGCTAAATAAAACCTATTCTTCATATTCCCACAATGACATATTACATATTGCTTGCAATCCCGGCTTCATCATGAATGGCAGTCACTTGATTAGATGCCATACCAACAACAAATGGGTGCCAGGTGTACCAACTTGCATCAAAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038496:ENSBTAT00000063039:22
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:
NO
A:
NA
C2:
PF0008415=Sushi=WD(100=46.2),PF0008415=Sushi=WD(100=42.4)
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:
AGGGTTTGGTTCCAAAGGATTCC
R:
AAGCCGGGATTGCAAGCAATA
Band lengths:
347-1655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development