BtaINT0072491 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68560496-68562603:+
Coord C1 exon
chr16:68560496-68560777
Coord A exon
chr16:68560778-68562435
Coord C2 exon
chr16:68562436-68562603
Length
1658 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TTTGGTGCTTTGTCTTACAGCCC
3' ss Score
9.83
Exon sequences
Seq C1 exon
TTCGACCAACTATATCCAACAGTGGTAGCCACCCTACTGAAATCATTGTAACTCGAGGAAAGAGCGTTTCCTTGGAGTGTGAGGTGGAAGGTGTTCCTCAGCCAGCAGTGACCTGGATGAAAGATGGCCGCCCTTTGACAAAGGGAAGAGGAATGGAAATAATGGATGAAGGTCGTGTGGTTCAGCTGAAGAATGTTCATGTGTCTGACACAGGCCGTTATGTGTGTGTTGCTATGAATATAGCAGGAATGACTGACAGAAAATATGACTTAAGTGTACACA
Seq A exon
GTAAGTATAAAGAGGCTCCTTAAGTCTGTTAACTGGCTGATATAATCTACAGCCTCCTGGATGGGAGATATAGACCTCAGGTGTTGAGTGTTTTATTTATAGTCTATTATTTTCTACTATTTGGAAAAGACCCTAATGCTGGGAATGATTGAGGGCAGGAGGAGAAAGGGGCAACAGAGGATGAGATGGCTGGATGACACGATGAACTCAATGGACATGAGTTTGAGCAAATTCCAGGAGATCTGGAAGGGACAAGGAAGCCTGGCATACTGCATTCCTTGGGGTTGCAAAGAGTTGGACACAACTTATGACTGAACAGCAACAAATTTCTACACACATATCACTTCTTTAGATCAGTCTCATCATTATCATGCTATGCCTGACCTCCCTTTTCTTATTTTGCTGAAATAAGCATATATCGGATATTCTTTTAGAAAAGCACATTGTGAAGTCGATAATTATCTTTTTCAAATACTTTTGATCCAATGCCATCCCAAGTGATATTCCTTGATTCTGTGTTTTCCTCATTAGCTGACTTGATAAGTGTAAACCTAGATTCCTTACAGCTTACTGACCCAGCTTCAGTTGGGCATAAGTTGTATTGAAATCAGCTTTACAATTCTAAATAATGAGCACAAATGTCAGTAGGAATAGATCAGACACACATGTACTCCTATTTATGTGTGATACCTATTTGTATGCATATAATTTGAATTGGGGTTTTTAAATCTATAGAATCAATGGTAAATCTAATAGACTTAGTTTTTTGACTTAATTCCAGTTAGAACATGCACAAAGTCCAGTATAGTTTGCAAGCAATGTGTGAAAGCTAATGATTGAAAAGAAATCAGTCTTATGTATCTTTTAGTTAGACTGTGGTTTTTTTTTTTTTTTTTTTCATTCTTTTTAACAGGTGCTTATTGCATTACTTGAATGTTTTATACTTTATTTGATAAATCCTCTAGGAAAGAACATTTAGGTCGGATGTATTAACAAGAGTGGCTGTCATAAAATTTCCTAGGCAAGACTGATGTTGAGAAATCAAGATCTCAGATTATGATAAATTCCAATTGACTCAGTCCTCTGCTTGCTTCAATTCTGTGAGACTCTGAAAGTAGAGCGCCACTGGCCCTGCTCTGTAACGAAGGAAAACATGATGGAGGGTAACTTTCCCTGGACTACTGAGGGCCATATAGAGGCACTCAAGGCCTGTGTGGAGCCTTGTTTCCTCTCCTTCTGGTGCTGGCTTAATTGGATTTTCATGCCAGTTCTCCTCTAAGCCAGCCCTTGCACTTGCCCAAGCCTGTTGGGTCAATGTGACCTGCCACCCCTCCTCAGACTATCCTGACTGCACTCTGCTCTTGGCCCAAACTTGTCTTCTCAGCCCACGTTGTGTGTTTCACATGTTTTTGTCCACAAGGCACACTTGCCCTCTAGGAGCTGGTCACTCCAGTCTTCTCTAGGGTTCTGGGTTCCCCCTCTTCTGCCCCTCTTAGTTGCTCTCTGACTCTCAGGCAGCTCCTTCACATTTTTACTTCCAGGAGTGTCACAGTCATCGTCATCATCATCTCATTGTTGTCATTGTTTATTTTGCTAGTGTTGCCCAGAAAATCATTTTTAAGAATAAACTATTTAGAATTTGGTGCTTTGTCTTACAG
Seq C2 exon
CCCCTCCAAGCATCATTGGAAACCACAGGACACCTGAAAATATAAGTGTGGTGGAAAAAAGCTCAGTGTCGCTAAATTGTGAAGCTTCAGGAATTCCCCTGCCTTCAATTACGTGGCTTAAAGATGGGTGGCCCGTCAACCTTAGCAGCTCCCTGCGAATCCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.168 A=NA C2=0.158
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=90.5)
A:
NA
C2:
PF0767911=I-set=PU(57.0=86.0)
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:
TTGGAGTGTGAGGTGGAAGGT
R:
GACGGGCCACCCATCTTTAAG
Band lengths:
348-2006
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development