BtaINT0102048 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020568 | NKX2-5
Description
Bos taurus NK2 homeobox 5 (NKX2-5), mRNA. [Source:RefSeq mRNA;Acc:NM_001046443]
Coordinates
chr20:4818457-4821534:-
Coord C1 exon
chr20:4821082-4821534
Coord A exon
chr20:4819570-4821081
Coord C2 exon
chr20:4818457-4819569
Length
1512 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTTTTCTGTTCCCCACTCAGAGC
3' ss Score
10.01
Exon sequences
Seq C1 exon
ATCCCGAGTTGGAAGGCGGGTGCGCGGGCGCGCGGCGGGCACCATGCAGGAAGGCTGCCAGGGGCCGTGGGCAGCGCCGCTCTCTGCCGCCCACCTGGCGCTGTGATTCGCGCGCTGCCACCATGTTCCCCAGCCCCGCGCTCACGCCCACACCGTTCTCGGTCAAAGACATCCTGAACCTGGAGCAGCAGCAGCGCAGCCTGGCCGCCGGGGAGCTCTCGGCGCGCCTGGAGGCCACTCTGGCGCCCGCCTCCTGCATGCTGGCCGCCTTCAAGCCCGAGGCCTACGCGGGGCCGGAGGCCGCGGCGCCCGGCTTCCCTGAGCTGCGCGCAGAGCTGGGCCCCGCGCCCTCGCCCGCCAAGTGCGCGCCTGCCTTCTCAGCCGCCCCCGCCTTCTATCCGCGTGCCTATGGCGACCCCGACCCTGCCAAGGACCATCGAGCCGATAAGAAAG
Seq A exon
GTGAGGAGAAAACCCAAGCTCCTTCACTTCTCTGGGATAGCTTTCGTCCCCAAACCTCGCGGCCCAGAAACTCTGGCGTGAGTACAGAAGAGGCGAGTGCCTGGGCGGATGGTGGAGCAAAGGGGTCTCCGAATGTGAGAAGTGAGGTTGTTGCCAGGGCCCCTGGGCGTCCAGTCGGAGGTTTAGAGGAAATGCTGGATCGTGGTTATCAGAAACAGGAGAGGAAAGAAAGGGAAAATATTTATATATTTTTTCCGGCCTAACAAAGCCCCAGGCGCCGCAGCCCTGCTCCTGGATCTGTTATGAAGTTGAAGTTGAGCGATCTGTTTGTGGTGGACACAGCAAGAAAGATTCTATTTTTTTAAAGGTCTTCTTGAGGATCTGACCAAAACCGCTGCAATTAAATTGCTGCACACCAGAAGTACTTTTACGCACAATTGGAGGAGGTCCAAGACCTTCTCTAGCCCACCCGTTTACCCGGGGTTTCTGGGGTCTTTCCTCCTTTGTGCCAGGAGAGTGGCGTCATTGAAAACAAGGATCTTGAATTTTAAAAAATGGGATACCTCGGACTCAAGAATGATTTTAGCAGCTTTCTTTTTCCATAACAATTTCCTCACGCGGCCAGAGCCTAGGGGGTCTTTCCGGGAAATAGAAAGTGTCTCGAGACGAAAGGCTTGTAGCAATGGAAGAGATGACTGAGGGAGGTGGTCGTATCCCCGCGCACATCCCGAGGTCGGGGGGAAGGCTGGCCGGGCAGTAGAGAATGCGCGGCGGGAAAACCGTAGCCCAACGCGGGGTTGGCAAGAACCCGGGGAGGCCGGGGGCGCGGGTGTAGGGCCGCTGTGAGCCCAGGAAGGGTCTTGTGAGCCTAGAAAGATTTGTCTAGTAGCAGAGGGAAAGTCCCGGAACAGCTGCCGGCGGGCACTGCGGCTTCAATTGGTCCATTCGGATTCGAATCCAATTCGATTTCAAGGCAGGTTCCAAGGCCGCCTGCCCACCCACTGCTTTTTGGGCGCTGCACAGTTCTCACAGCATTTGAACGGGAGCCTTCGATAGATCACCGAACCAACTGCCTATTGACGTTCTATTTCTTCGGTTGCCGTAATTTTGAGACAGTGTGACCAATCCTAGGGTGAGGCCTAGGTCTCCTTCCTTTAACTTCGCAAACCAAAGTCTTCCTAATCTCATTCACTCCAGCGCATCACTGAGCTTTATTTTCTTTGCCGCCTATCTTAAGTCACTGTCCATCTGTCTCACCAGAATGTGACCTACCCGAGAACAGAGACCTCTCTTGTTCTCCAGTGCCAACAGCCGTGCCCGGCACATAGTAGGCAATCAACAAAAGCTGGCTGTCGAGCGGAAGCCCAGTGTACCGTACAGTCTGCCGCAGCCAAGCTAGGGGCTTCAGGCTGGACAGGGGTGGCACCCACTGGAGCCCATCAGCCGGCGAGAGCTCCGGGGGGTTGGGTGGCCGTGACACAGCGTCTCTCTGCTTTTCTGTTCCCCACTCAG
Seq C2 exon
AGCTGTGCGCACTGCAGAAGGCGGTGGAACTGGAGAAGCCAGAGTCGGACAGCGCCGAGCGACCCCGCGCACGACGGCGGAGGAAGCCGCGCGTGCTCTTCTCGCAGGCGCAGGTCTACGAGCTGGAGCGGCGCTTCAAGCAGCAGCGGTACCTGTCGGCTCCCGAGCGCGACCAGCTGGCCAGCGTGCTGAAGCTCACGTCCACGCAGGTCAAGATCTGGTTCCAGAACCGGCGCTACAAGTGCAAGCGACAACGACAAGACCAGACTCTGGAGCTGGTGGGGCTGCCCCCGCCGCCGCCGCCGCCGGCCCGCAGGATCGCGGTGCCAGTGCTGGTGCGCGATGGCAAGCCTTGCCTGGGGGACTCGGCGCCCTACGCGCCAGCCTACGGCGTGGGCCTCAACGCCTACGGCTACAACGCCTACCCTGCCTACCCCGGGTACGGGGGCGCGGCTTGCAGCCCCGGCTACAGCTGTACCGCTGCTTACCCGGCCGGGCCGCCACCGACGCAGACGGCCACGGCCGCCGCCAACAACAACTTCGTGAACTTCGGCGTCGGGGACTTGAACGCGGTACAGAGCCCCGGGATTCCGCAGGGCAACTCGGGAGTGTCCACGCTGCACGGCATCCGAGCCTGGTAGAGAAGGGACCGGTCTGGGAGGCCTCCGACCGATCCCACCTCTCAAGAGAGACACTGACTAAAGAGGGGAGAGGGAGGGCTCCGGACACGATCCTGCGATCCCTCGGATGTCACATGCACTCCCACGGAGGCTTCGGAGCTTTTCCCGCCCCGTGCGCCTTTGTTCCCCGAGAGGGAGAGTTTGTGGCCAGGTTTACGCAGCTTGTGGTGAGTGAAAAGGCAGCCTGGTGCCTAGCTGTGGCCCCAGGAGTGCCCTCCGAGCGCCCAGGAGCATCCCTAACCGGCCGAACACCAGCCCATTGGGACTGGGAGCCCGGGCGCAGCAGCCTCGTAACGGCCGCCTTTCCCCAAGCCTGGGCCGGGCGCCCGGGCCCTTGCTGCCTTGCGGCTGCCCCCCGCCCCCACCCGTATTTATGTTTTTACCTGTTTCTGTAAGAAATGAGAATCTCCTTTCCATTAAAGAGAGTGCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020568:ENSBTAT00000027402:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.369 A=NA C2=0.263
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=26.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTATCCGCGTGCCTATGG
R:
CCCACCAGCTCCAGAGTCTG
Band lengths:
345-1857
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]