BtaINT0072524 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68645739-68647802:+
Coord C1 exon
chr16:68645739-68645895
Coord A exon
chr16:68645896-68647680
Coord C2 exon
chr16:68647681-68647802
Length
1785 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGCTTTGAAATCTCTTCTAGGCT
3' ss Score
8.51
Exon sequences
Seq C1 exon
TTCCTCCATCCATTGCTCCGGGTCCTACCAACATATCTGTAACAGTAAATGTTCAAACCACTCTGGCTTGTGAGGCTACTGGCATACCGAAACCGTCAGTCAACTGGAGGAAAAACGGGCATCTTCTGAATGTGGATCAAAATCAGAATTCATACAG
Seq A exon
GTAAGGAGCAATTTATCTGGAAAATTCCACCAGCTATTTAGAAACATATTTTTCAAAGAATTAACATTTTCGCTTTATCAATGGGGACAGAAAATGTATAAAGTACGAAGAACTAGCTAGTATGCAGAGAGTATATTATTTTTTTCTTAGTATTGAATTAGTTTTTCAATCTAAAGTATTTTTTCTGAATTACAGGTACAACTTCTCTTTCCATAAGCCCTGTGGATGACTGTCAGTGAGCTCTATAGCATTAAATTTCCATTCTGCTGCTGTTTTTAGCACCTTTCATAATTTTATAATGACAAAGGATAAAAACATCATTTAGTATAAAAGAAAAAGTACTCTTTAAAAATAATATGAGTTTTAGTTGCAGAATAAAAATCAAATTTTATACCTTCAGATACAGTGTAGGTATTTGGCAGCATGTGTAAGGAGAAAGTGGAGAAGGCAATGGCACCCTACTTCAGTACTCTTGCCTGGAAAATCCCATGGATGGAGGAGCCTGGAAGGCTGCAGTCAGTCCATGGAGTCGCTGAGGGTCGGACACGACTGAGTGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCTATGGGGTCGCACAGAGTTGGACACAACTGAAGCGACTTAGCAGCAGCAGTAAGGAGGAAGAATAGCAGTTTCACCAATTTTCTGTACTCTTCCAGCTTTACTACCATTCTTCTTACTATATCATATTTTTAAAGACTAACCTTAAAAATACTACATATTTCTGATTCCTTAGATGAGCATTTCTTGTGTTAATAGATATCTTGTCAAAAGATTTGCTATATCACTAAAAACAAGTTTTCATAGACCTACCCTGATAAAAATTCATTCTGTTACATCTGAAAATATAAATTAGGAGGGTTTCAGTGGAAAATCTGTTGCGTCTCTTTCTCATCCTTTTAATCCTTTGGCATTGGGGGTTTAATGACTTGAAAGCATACTCTATGTGGAAAATGCCAATGCCCTTGAATTAAGAAGCAGGTCAAATCTGTTCCCATTGAATCAAATTATTCCCATCCATCAGTGCACAGTTTGAGGTAAGAAAATAGATATTCTTATTTAGATTACTTTAAATAATGTATGTGTGTTTACTCAGCCTTTTGTATATTTGAAGTGATTCAGATAACTTTAGTTTTGAGTTTATTTCAAGTTAGACTCTGATTTATGTACTGTGCATCTCCAAGGTATCCGCCACATGTAAGGAGACATGTGAAGCAGGGAAAGCTGCAAGACAGACTTATGGTTACCTATCAGTCAGTGGAAATAATCAAATTCCAAGCTGCAAAGTTACTATGACATTTAGAGATCATCTGTGTGAAGCATCTGAGATGGCACCAGGAATGTATCTGGTGGTCAGTAAACAGCGGCTATCATCAGTGTGCTCATTTCACTGTATTTCACCTAGGAGAGCATGGTTGGTCACGCTATCAGCATTCAGAAACTGCAGGATTCCCTCTTAAGGCAATCATTCTACACCACTGCTTCCTGCAGATGATGAGGTTGAGGCCCTGTTAACCCACTGCCATATAAACTTAAAGTCTGATACATAAAATGATGCTCACTTTAACATTTGAGGGAAGAGTTCTCTTTCCCTCAGTTCACAACATGGTACCATGTTGAACCAACTAGAAACATTTATGAAAACTGATATATAGCACCTCATTGCTTTGAAATCTCTTCTAG
Seq C2 exon
GCTCCTTTCTTCAGGTTCACTGGTAATTATTTCCCCTTCTGTGGATGACACTGCAACCTATGAGTGCACGGTGACCAATGATGCCGGAGAGGACAAGAGAGCTGTGGATCTCACTGTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:76
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.113 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(55.6=94.3)
A:
NA
C2:
PF0767911=I-set=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTCCATCCATTGCTCCGG
R:
GTGAGATCCACAGCTCTCTTGT
Band lengths:
271-2056
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development