BtaINT0029222 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009876 | C4BPA
Description
Bos taurus complement component 4 binding protein, alpha (C4BPA), mRNA. [Source:RefSeq mRNA;Acc:NM_174252]
Coordinates
chr16:4793863-4795606:+
Coord C1 exon
chr16:4793863-4793963
Coord A exon
chr16:4793964-4795451
Coord C2 exon
chr16:4795452-4795606
Length
1488 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTCAAATTGAGTTCTTTCAGCAG
3' ss Score
0.34
Exon sequences
Seq C1 exon
AATTTTCCTAGTGGCCAAGCCCAGAGCTCATGGGGTAGGGGTGGAGTTACCTGCAGCTGATAGCAGGTGGAGGCCTGAGTGTCAGAACTGAGTTTGCAAAG
Seq A exon
GTAAGATTAGACGAGTCTTTGCTCAGTGAAGAAATTGGAGCCCTCCGTGTCGTGTGAAGGGCCACTATGAACTTTTTTCCCCTAAATGTGGGACAGAAACATCTTTGAGGCAAATATTGAGGGGACCCCTTTTATCTAAATGGATATGCAATTAATATGAATTATGGACACATGGAGAGAGTAGAATCATATGGATCAAACAGAAGAATCAGAATAAAAGAAATTCAGTATTTCATTGGGGCTTAACTTCGTGTGTTCCTTTGAAGACAAAGACTAATTCTAATGTAAATTTAAGATACACTTTTTTTTTTTTCCAATGGAACAGGAGTGTGGTGAAGAGAAAATGTTCTTCATGATTTAGCTTTAAATAAGTCTTTAAATAGTCTAATTAAATAATGAAAGTACATTTGTCACATATATTTTTATTTATATACCTATATATATATATATCTACATATATCTATGTTGTTATTGTTTAGTTGCTAAGTCATGACCATCTCTTTGCGACCCCATGGACTGTAGCCTGCCAGGCTTCTTTACCCATGGGATTTTCCAGGCAAGAATACTGGAATGGGTTACCATTTCCTTCTCCAGGGGATCTTCCCGACCCAGAGATGGAATCTGTGTCTCCTGTTTGGCATGTGGATTCTTTACCGCTGATCCACCTGGAAAGCCCCTACATATATCTATAAATAAAACCATCTTTTCCCCCCAAAACTGCAAATTGCTTGGTTTATTGTTTCAGTTGATAGTTGTCATGAGGAACTGCCAATGTTATACATGATGATCCAACTCTTTTTTCTCTATCTTATAATCTTCCTGCTTTTTGTTTTGTTTTAAATTTATTTCATTTTCTCTAACTCCTTTGCCATTTCCTTGGTCTGATCATCTCTGTGGCTCACCTGGCCAACTACAATAGTCTTCTTAATCAATCTCCCTGTTTCTCCTCTGTTCATTTCAATCTATCATGTATATTTAATACATCCACTCTAGTGATATTAAGATACAATGATGTATCACTCTAAGGACATATTAAAAACAAACACACCAAAAACAAAACCAAATCAAAACAAAACCGAGAAACACTGGCTCTTTACTCTCTAAAGAGTAGCGTCCATAAATTCCTAACCTTGGCCCTTATGTCCCATTCAGACACACCTGTGAGCTGCCTCCTGCTTAACAACCATCTGTAACACCTTACTTTCCAGCCAAACTGTAGTGCTATGTACTGTTCCCCAATATGCCCTGCCTACATTTTCTAACTTTTGCAGAATACCTAACTCAGATTAAGCTACCTCCCATCTCTCCACTTGGAATGAATCTCTCTCATGAGCAGAGTGCTTCTTCAGAGGCTAACACCTGCTGTTTCGTGTCTTTTCTTCCAATTCTAGGCTGTAATTTCTTCAAGACATGGATCCCATAGCATGATCCTAGTGCTTTATGACAAGTAGGAATTCAATGATTGTTTTTCAAATTGAGTTCTTTCAG
Seq C2 exon
CAGAAAAGTGTCAATGAAGCATCAGCGAGTTCCAGTTATGATCCTTCATAGCAAGGGGACAATGGCATCCTGGCCCTTCTCTAGGCTGTGGAGTATCTCTGATCCAATTCTGTTCCAAGTGACCTTGGTTGCTACTCTGTTGGCCACTGTTCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009876:ENSBTAT00000050299:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
GCCCAGAGCTCATGGGGTAG
R:
CAAGAACAGTGGCCAACAGAGT
Band lengths:
238-1726
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development