BtaINT0102046 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021397 | NKX2-3
Description
Bos taurus NK2 homeobox 3 (NKX2-3), mRNA. [Source:RefSeq mRNA;Acc:NM_001034676]
Coordinates
chr26:20400227-20403772:+
Coord C1 exon
chr26:20400227-20400742
Coord A exon
chr26:20400743-20402224
Coord C2 exon
chr26:20402225-20403772
Length
1482 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TTGTTTTGCTTCTTTCGCAGAAA
3' ss Score
9.93
Exon sequences
Seq C1 exon
AATGGAGGCGATTTAGACTGGAGTGGGACCGCGTCTGTCAAAAGCCCGACTCGGCAGCAGCGGCGGAGTCCAGAGGAGAGCTGGAGCCGCCGCGCTGCCTCCCCGCCCCCGCCGGGATTTATTGAGTATTTGGACTGGACAATTAAGTGGCCCTGATGATGTTACCAAGCCCGGTCACCTCCACCCCTTTCTCAGTCAAAGACATTCTGAATCTGGAGCAGCAGCAGCAACAGCACTTCCACGGCGCGCACCTGCAGGCGGACTTGGAGCACCACTTCCACTCGGCGCCCTGCATGCTGGCCGCCGCTGAGGGGACGCAGTTTTCGGACGGAGGGGAGGAAGACGAGGAAGAAGAGGGCGAGAAACTGTCCTATTTGAACTCACTAGCTACAGCCGATGGCCACGGGGATTCGGGGCTCTGCCCCCAGAGCTTTGTCCACACGGTCCTGCGAGACTCGTGCAGCGGGCCTAAGGAACATGAAGAGGAGCCCGAGGTCGTGAGGGACGGGAACCAAA
Seq A exon
GTGAGTAGAGGGGGAAAGGAAACACTCATGTGGAGCAATGGCGGGATGCCCGCAAACAGCCCACCAACCTTGTCGGCACGGCTGCCCGCCTCTTTAGCTCCTGGCTGGTGTCATGCCAGTTCCTGGTCAGCGACAGCTCCGCAAAACTCAGATGCTGCAAGGGAGCCAGGGCGGAGGGAGAAGGCCAAGATGACTCCGCCAACTACTCCCCCCAGAGGGAGGAGGCGATGCAGCCCCGGAGGTTATTGCTACCCTGATGCGGATAAGCAATGTGGGCTCAGCTGCCGGGTGCTGACAACTGTAGCTCTTCCCCAGAGCTAGAGGGGCATGAGCCTCAACTTCTCCCACTTTCCCTCTAGCGTGAGATGCGTTTTTTGAGGCCAGGGCAGCCGTTCTCTCTTCTCGGAAAAGGTAGTCCAAGCAGATTGTGTGCCTGGTGTCCGGAGGGCGCAGGAACTTAGGTAGAATTTTAGCGGGGGTGCTTTCCTCACTTCTCCGCCTGGAACTCTGCGTCCTCGCACCCGTGGCACCCGGCAGAGAGCGAGCGGATGGTGGGAGAGCGCATGGGAACGTAGTTCATTCCTCACTCGCACCCCTGAGGCAACCGGCCTTTTTGAAAATCTGTAACGTTTTGCTTTGTGTCCCAGATTGTGTGGCTTCGGGCTGAGTGAAAAACGCGCCGAACTTAGATCCTGTCTGCTCAAGTAGGACGGGAGGTGAATTGGGCAGGGCAACAGAATAACTGAATAAAGCCTCCAAGGAAGTGTTTGTGAGGAGACAGAGCCAAAAGAATCTCCTTCCCCAAGAGAAGGTTTGTTGTGGCGGAAGCCAAGGCCTTTGCTCTGACAGCTCCCCTGGGCCTAAAATCGACATGAAACTAAGTCAGTCAGTCAATCAAATTTCTTTTTCTTTCTAAGGTATCGGTTGTCGTTACTCAGACACTCATTTGTGGGTAGGTAGGCGTTTAAATGTAAACAAACAAACAAAAAAACAGTTCCTGGGCAATAAGCAGTACACTCAGACATTTCTAAGCAGGAAGATTTTCGCACATCGCACGCATTTCGGCCGCCAAAAACCAACATGCCTCTCACACCTTCAGCTATTTATGACGGAAAAGAAGGCAACCGAATTTGCAAATATTGGAGTTATGTAGTTACAAACTTTCATCCTGAAAATAATCATTAGCAAGCCGAGCTGCACATTTAATACAGGGTAATCTCTCGCAGATGCTGAAGTTCTAAATAAACGCGTGCTAACTACCCCTCCCCACACTATGTGCCTCCACCCGTCAAGGACGTGGTGAGGGGCCTTGGGCGATCGAAGGGTCCCACGGCGCCAGAAGTCACAAACCTTCCCCAAAACCCAAGCAGTTATTACTGCACGCTCCGCGTTGCCACCAAAAAGGGTCACAGTGCTCCTGGACCGGAGCCGCGGAGAGGCCGGGAACAACTAAGAGACGCTGTTGTTTTGCTTCTTTCGCAG
Seq C2 exon
AAAGCTGCCAACTGAAGAAACCTCTGGAGGCGGCCGGAGACTGTAAGGCGGCAGAGGAGAGCGAAAGGCCGAAGCCACGCAGCCGCCGGAAGCCCCGGGTCCTCTTCTCTCAAGCCCAAGTCTTCGAGCTGGAACGCAGGTTCAAGCAGCAGCGGTACCTGTCGGCGCCAGAGCGCGAGCACCTGGCCAGCAGCCTAAAGCTCACGTCCACCCAGGTGAAGATCTGGTTCCAGAATCGCAGGTACAAGTGCAAGAGACAGCGGCAGGACAAGTCTCTGGAGCTGGGCGGGCACGCGCCCCCGCCGCCGCCGCGCCGTGTGGCGGTGCCGGTGCTGGTGCGGGACGGCAAGCCGTGCGTCACTCCTGGCGCGCCAGCCTACGGCGCGCCCTACAGCGTGGGCGCGGGAGCCTACTCCTACAACAGCTTCCCCGCCTATGGCTATGGGAACTCGGCAGCCGCCGCCGCAGCCGCCGCCGCTGCAGCCGCCGCCGCCGCGGCCTACAGCGGCAGCTATGGCTGTGCGTACCCGGCAAGCGGTGGCAGTGGCGGCGGCGGCGGCGGGGCCTCTTCGGCGGCCTCGGCCATGCAGCCCGCCTGCAGTGCGTCTGGAGGCGGCCCCTTCGTGAACGTGAGCAACCTGGCCGGCTTCGGGGGCGGCGGCGGCGCGCAGCCGTTGCACCAGGGTGCGACGGCGGGGGCCGCGTGCGCTCAGGGTACCTTGCAGGGCATCCGGGCCTGGTAGGGACCGGGCAGGTAACGCGGCAGGCGACCCCACCGCAGCCTGGCGCCGCGGGACTAAAGGGCGAGAAAGGCTGGATCCAAGGAAGGACCAGGTCCCCTCGTTAAAAAATATAAATATATATACATAAACGTCTCGCTCCCCAGGGCCTCGGAGCGCAGCTTACACGAAGTCCGGGGAAGGAGGCTCTGGGGCGAAGAGGATGCGCCTGGGCCTACATGGAGACTATCTCTGAGGCAGAAAAGCTGGCTGGGTGCCTGGAGGACAATGGCCCCAATCTCGGCTCCAAAGGGAGTGCGAAAGGCTGGGACTCAGGCTGCCAGTCGTCTCTCCTAGAGCAAGAAGGGCTTCTCTTTCTCGGCCTTCTCGCGGCCTCAGCAGAGCGCTGGCGGAAAACTCAAGGACAGAGAACAGCATGAAGGAGAGAAAAATGGGCGTCGTGGCTTGATAAATCCCCAGGCCCTACCGACCCTCTGCTCACTTTGCAGGGCCGGAGTGCCACACCACAGTCCATTTTCCTTTTCCCAACCGCCTGCCCTCCGCAACAGATACCTCGGCCTGGATCTCCAGATTGTCAGGAGGCGTAGAACTCTGCAAGAAAAATCAGCGGAGCGAGATCAAAAGTTGGGGGCTTGAACAAATCTGGAACCTAGGGGCCCACCGGAGGTGTTACCGGCTTTCCTTCTGTTTCCTATTCTGTATTCAGCACATATAATATATATATATATATAACTAAATATATCCACACGCCATGTACACACCCGCTGCCATACACTACAGGAGTCAATAAACAAGGTGCAATATTTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021397:ENSBTAT00000028522:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.736 A=NA C2=0.251
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGCTTTGTCCACACGGTC
R:
CTCTTGCACTTGTACCTGCGA
Band lengths:
347-1829
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]