BtaINT0087868 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019839 | LTBP1
Description
Bos taurus latent transforming growth factor beta binding protein 1 (LTBP1), mRNA. [Source:RefSeq mRNA;Acc:NM_001103091]
Coordinates
chr11:15946182-15947670:+
Coord C1 exon
chr11:15946182-15946331
Coord A exon
chr11:15946332-15947488
Coord C2 exon
chr11:15947489-15947670
Length
1157 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
CGTGGTTTGGCTTACTGCAGATG
3' ss Score
7.5
Exon sequences
Seq C1 exon
GTTTTCTGAACAGCTTTGAGGAGTTGCAGGCGGAAGAATGTGGCATCCTCAATGGGTGTGAAAACGGTCGCTGTGTCAGGGTGCAGGAAGGCTACACCTGCGATTGCTTTGATGGGTATCACCTGGATATGGCCAAGATGACCTGTGTCG
Seq A exon
GTAAGAGCCATGTGTATCTGACGGGAAATCATCCTTTTCCTGAGACGCCCTGTGGCTGGACATCATGTAGTCTAGTACATTAAAGATTTGCAGCGTTTCAGTTTGGGAAGATGAGAAAAATTCTGGAGGTGGATGGTGGTGACGATTGTGTAACAATGTGAAGGTACTTACCACCACTGGACTATCCACTCAAAAATGGTTAAAATGGTCAATTTTATGTTCTGTATATTTTACCCTGATTTTTAAAGAAGTACTTAAGAATTCATACAAATGGTACATATGGAGGAAACACCAGAACATTTGGGGTAATTAGACACTTTTAAATTGAGCTTTTGACTCAGTAGCAAACAGTGTTTTCCCTGAACACCTGATGCCAGCATGAGGGACATATAGATGAAAAAAAAAATGCTTCCATTTTGGAGAAAGTGTTTTTTTTTTTTTTTTTAATAAAACTCTCACGTAGCCTTCTCTTTTACCTTTAAGAGAACAGTAAATGGGGTTTTTTTCCTTCCTGTGTAATTGATGCTGTGTTCCTGAGCCTGCTGGCCTCCATGCTGAAAGACCTTTGACTGCAGGGTGTTGTTTTTTTTTTCCCCTATTTTTGTGGCTGTTTTTCTCCCTCCTGTAGTTTTCCCACTTCAGTTTTGTTAGTCTCAGTCTGTGGTGGTCCAAAAATAGGTAACCCAGGTTGTTACACGTGTTTCAGGGGCATAAAAGACTTTCTTTCCTGTGGAAAGAAATCTAAGAAAGTAACTTAAGCCTTGAGACAAGCTTCTTGGAGGCTCTGTATTTCTCTTGACAACCTAACTGCTCTTCTACATCTGCAGAAAGGGATTTAGAAGTAACATAGTTCTAGTTTTCTTGACTATAAAAACTCAAGCTGACAAAATGGTCCCTTTATGGTCAAATGGTCCCTGTTATGTCAAATAACAGGGGAGTATCCAAGGGATTCTAGAATTTCTTTCCCTTTTTGCGATCTAGAAGGTCATATTTACCTTGCATAAACAGACAGTAAGAGGAAAGACTACACAGCTTACCGTGGAGAGAGCACGGAATAGCCGGCTGTGTTTAGGCAGGGCCTCAGGTAAGCTGTTGATTGTTTCTCCTCCCGGAGTGATGGGAAAGCTTGCTTACCTCCGTGGTTTGGCTTACTGCAG
Seq C2 exon
ATGTCAACGAATGTGATGAGCTGAACAACCGGATGTCTCTCTGCAAGAATGCCAAGTGCATCAACACCGAAGGGTCCTATAAGTGTGTGTGCCTGCCGGGCTTTGTACCTTCTGACAAGCCAAACTACTGCACTCCATTGAATACTGCCTTGAATTTAGAAAAAGACAGTGACCTGGAGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019839:ENSBTAT00000026435:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=58.8),PF062476=Plasmod_Pvs28=PU(40.0=66.7),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF062476=Plasmod_Pvs28=PD(58.8=82.0),PF0764510=EGF_CA=WD(100=72.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGAACAGCTTTGAGGAGTTGC
R:
ACTCCAGGTCACTGTCTTTTTCT
Band lengths:
326-1483
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development