BtaINT0041203 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37088246-37090149:+
Coord C1 exon
chr19:37088246-37088466
Coord A exon
chr19:37088467-37089954
Coord C2 exon
chr19:37089955-37090149
Length
1488 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
ATCTCCCCGTCTTGCCCCAGTCC
3' ss Score
7.83
Exon sequences
Seq C1 exon
GCAGACGGGAGTTTCTCCTCGGGGTCGGAGCAGGAGGCACGCGGAGTGTGAGGCCACGCATGAGCGGACGCTAACCCCCACCCCAGCCGCAAAGAGTCTACATGTCTAGGGTCTAGACATGTTCAGCTTTGTGGACCTCCGGCTCCTGCTCCTCTTAGCGGCCACCGCCCTCCTGACGCACGGCCAAGAGGAGGGCCAGGAAGAAGGCCAAGAAGAAGACA
Seq A exon
GTAAGTCCCAAACTCTTGGGAGTCTAGGGCTGCTTGCTCTCCTGCCCTGCGCTCGGTCCCGGGGGTCTGCGACTTAAACTGAGACTCGGGATGCTCCGGAGGCTCAGGGATGGAAGGAAGATGGTGAGGGCTCTTCCTCGGTGCCCTCTCTGCGACGGGGTGTTGATGAAGGCCCCCCAGGAGTAAGAGGGGAGGATGCTGCACGGCACGAATTGGCGCAGGAGGAGTTCTGAGCGCGCACTGTGAAGTACAGAGGGAGAAATAGGGTCTGGGCACCGGTTTGGGGGAAAGTACGTCGAAGATGGGATGGAGGCGCTGAGTTGGGAAATTGGAGTCCAAGATGTAACAGTGATCAGGAAGGCTATGGGATGATTCATCAGGAAAGACTGTTTGCCCTCTCTGCGGGCTAGCAGTGTTCCTGGGGCCGCGGAGGTCTTGGACTGAGGGGGGAGGGGGCGCAGAGAGTGGGCGGGTTGAATGATGAGAAACTTTGGCGCGGACTTGGCCACGCAGGGTCTTTGCGCCCTCTGCTGATCTACACTGGGCAGTGCGCGTCCTTATCCAGCGCTTCCCCGCGCAGGAGTTGGAGCGGGAAGACCGGGATTGTTGCTGGGTGTGGACCCCACCTCTAGATCTGGAAAATAAAGCTGGAGATGAGATAGCCCCTGTCTCTAAAAGAAATAGCTAGTTTGGGGAAATTGCTTAGTGTTGCTCTGCCACCTAGTGGCCGTCTGGGTAGAAGATTATGCGGTGGGCGTGGTTAACTAACCACTTACTGTTGCGGACTTTCTGGTTCTTTGACTAAGAAGTGACCCGGAGCACTGGCTGGCTTTGAGAAACGGGGGTTGCCCCTGAGCGGGGCCTTTTGAGATGTCTGGGCGCCGGAGGTTAGGGCGTACCCTATTTTTACCGTACATTTCAGGTCTCTGGGCGGGATCCCACGCCAATCAGCCCCACCCCATCCTCTTAGCCCCGCCCACGCCGTCCCACCTGCCCCGGGAATGGGGCGGAATCTGGGTTGAACCTCCCATCTCTCCTCCCATTTTCCTCTGAGGTCTTCAACCAAGGTCACGCCCCACAAGCCTGCCCTCGGGATGGGGCTCCTCTCTTACCACTCCTCCATCCCCCAGCCCCACCCCCACCCAATGGCTTTTTATTTCACTTGGCTTCAGCGCCAATGGGCTGAGGTTACAGTTGGAAGCGACCCTGGCCTAAAGCTTTGTTTAAATTCCTGAGAACTGGAAAGAGTTATAGCTGTCCTGGCCAGGCGCCTCGGCCCTGTCACTGGCTCTGATGAGGAGCAGATGAGCGTTTAAGGATTTGGGGGAAGGAAAAACAAAAGGACAAAAAATGGAAAGGCGGGAAATGGAAAATCTAAATGTGCCTCTAAGACCGAAGGGAAGGGACGATGGGGTTGGTATGCCTGGAGACCCGAGGTGGGGGACTCGCGCGCCGCTGACAGCCCCCCATCTCCCCGTCTTGCCCCAG
Seq C2 exon
TCCCACCAGTCACCTGCGTACAGAACGGCCTCAGGTACCATGACCGAGACGTGTGGAAACCCGTGCCCTGCCAGATCTGTGTCTGCGACAACGGCAACGTGCTGTGCGATGACGTGATCTGCGACGAACTTAAGGACTGTCCTAACGCCAAAGTCCCCACGGACGAATGCTGCCCCGTCTGCCCCGAAGGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.242
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009313=VWC=WD(100=84.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTCTCCTCGGGGTCGGAG
R:
AAGTTCGTCGCAGATCACGTC
Band lengths:
342-1830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development