BtaINT0073195 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016030 | HOXD10
Description
Bos taurus homeobox D10 (HOXD10), mRNA. [Source:RefSeq mRNA;Acc:NM_001099105]
Coordinates
chr2:20828934-20832040:-
Coord C1 exon
chr2:20831257-20832040
Coord A exon
chr2:20829901-20831256
Coord C2 exon
chr2:20828934-20829900
Length
1356 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGT
5' ss Score
7.13
3' ss Seq
TCTCCCTTTAATTTTGTTAGAGG
3' ss Score
4.45
Exon sequences
Seq C1 exon
CAAAGGACACAATCTCTCTTCTTCAAATTCCTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTTTTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCGAGCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTATGGAATGCAAACCTGTGGACTGCTCCCGTCTCTGGCCAAAAGAGAAGTGAACCACCAAAATATGGGTATGAATGTGCATCCTTATATACCTCAAGTAGACAGTTGGACAGACCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAGCAAGTCCCCACTTGCTCCTTCACCACCAACATTAAGGAAGAATCCAATTGCTGCATGTATTCTGATAAACGCAACAAACTCATTTCTGCTGAGGTCCCATCGTACCAGAGGCTGGTCCCTGAGTCCTGTCCCGTTGAGAACCCCGAGGTTCCTGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAACCCAAGAGTACAATAACAGCCCCGAAGGCAGCTCCACAGTCATGCTCCAGCTCAACCCTCGCGGCGCGGCCAAGCCGCAGCTCTCGGCCGCCCAGCTGCAGATGGAAAAGAAGATGAACGAGCCAGCGAGTGGCCAGGAGCCCACCAAAGTCTCCCAGGTGGAGAGCCCCGAAGCCAAGAGCGGCCTTCCGGAAGAGAGGAGCTGCCTGGCAGAGGTCTCCGTGTCCAGTCCCGAAGTACAGGAGAAGGAAAGCAAAG
Seq A exon
GTCGGTATGAGCAGAGTTGTCACCCCAGCGGGGCGCGCAGCCCTGGAACCGGCAGAGAGAGGGAACACCCGGGTGCCCAGTGCTGAACCGGCAGCCTGGGGCCCCGACTGGCAGGTGCCTCTCCTCCCGTCTTTTAGAAGGGCAGTCTTAATCCCGAGATGGTTTTCTCTTCTGCCGCGCTGCCCTGACCCTCCTGGCTAGTCCTGGCCCCGTGCTGATGGCGCCTGGACAGAGGAAGGGCTTTCCGGGTTTATTTTTCCTGAGCTAGACCTGAAATGCAACAAAAGAGCGCAAATGAGACCTGAGGCTGGTAAACGCGGCCCCAGAACCTCCTTTCTCCCGCTCAGATTTGCAGTCCCAGCCATGCCTTTCACTCAATGATGATTTTAAGGTGGTCCAAAGTACCGTGTTCGTGTTCAAGTGTATGCACCCCGCATCCTGCGAGCTTGGGGACAGCAAGGGGAACGAGATGGCTGGACCAGTTGGTGCTTGGGCTGGAGAACAGGGCTCCCTGCCTCTGCGGGGCTAGGTAACCTTGGCTTTGTCTGGGGAAAGTGCGGAAAGCTTTGCAGTCCTTTTGCAAAGGGAGCAAAGGCATAAGGGAGGGAGAATGGAATGTGCATGGCCCACCCGGCAGGGCCAGCCTTAGGGCTGGATAGGGCAAAGAGCCAGGGGCTCTGGATTTTCTGCCCCTGATCCTCTGCCCCAGTGCTCAGAGTTGGGCCACAGCAAGGAGCTACATTTCTCATTTCTGGGAGAATGCTTTTGTGTGGGGGCAAGAAAGCACAAGAATTCAGGAAATTCTGGGGCATAAAACTATGCCCAGGCAGGGCGGAGAAGGTGTACTTGGTTCCTCTGGTATCTTTTGAAAGAGAACTGGTATCTCTAAGCCTGACTGTGGGGCTCCCCACCTGCCTGGGAGAAGTGGGGAAGAAGTGGCAGGTTTGGGGATCCGAGGCAGCAGTGGGATTCGTAGGCTTGTCAGACTGTGGTTTGCTTCTTCCACTCTAGCCCTGTTGTGAGATGATCATTTAGAATGTTGCTGGTGAGATTCTGAAAGTTTACTATTGTACTAATATTTTGTGCAGGTCAGAAAGTAGAGAGAGAGAGAGAGAGAGAACGCTGACACAGACGGCAAGAATACCCACCCATTTGTGTCATTTTGGGTACTTTAACTAACCTGGCATCATTTACAAATATCTTTCAGGGCCCACCTCATGTGAGTAATGTTTAATGCAAGCATTTCCCAAAGTGGCCTGGCTGCCAGCGGGGTCATGGCCAAGGGTAAATTTGAACAGATTGAGAGAAAAAAAAAATTCTTGATTTTTTTTCTTCTTCTCCCTTTAATTTTGTTAG
Seq C2 exon
AGGAAATCAAGTCTGATACTCCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGCCCTTACACTAAGCACCAAACGCTGGAATTAGAAAAAGAGTTCTTGTTCAATATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACCTCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTCAAGAAGATGAGCCGAGAGAACCGGATCCGAGAACTGACCGCCAACCTCACCTTCTCTTAGGTCCGAGGCCCGTCAGAGGCTAGGATCGGAGAGGGGCGTCGAGTTCCAGGGCCGAGTGCTGGAGGACTGGGAAGGCGGAAACAAAACCTTCAATGCTCTTTGTTTTTTGAATTTTTTTTTTTTCCTGCTAGAATGTGACTTTGGGGTCATTCTGTTCGTGCTGCAAGTGATCTGTAATCCCTATGAGTATATATATATATATATATATTAAAAAAACTAGCACGTGTAATTTATTATTTTTTTTCATCGTAATGCAGGGTAACTATTACTGCGCATTTTCATTTGGCTCTTAACTTATTGGAACTGTAGAGCATCCATCAATCCACTCGTCCGTCCAGCAATGTGACTTTTTCATGTTTTTCCTAACACAAAAGGTCTCTGTGTGTGGTTAGTCCATGAGCTCATGGCGTTTTGAATACATCCAGTACTTAAAAGTACTTAAATTACATATATATTTAAAAAGATTAAAACCCACAAGCTTTGGGGGGAGGGGGACTAAAAAAGCACATTACAATGTATCTTTTTGCAAATGAGTTTAGCAGTTGTCCTTGGTGAGATGGAATATTGACTGACTTTGCCTTGTAGCCTTTCCCTTGTGGTGCATCTGTGGTTTGGTAGAAGTACAACAGCAACCTGTCCTTTCTGTGCATGTTCTGGTCGCATGTATAATGCAATAAACTCTGGAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016030:ENSBTAT00000021334:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.518 A=NA C2=0.293
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=61.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGTCCCGAAGTACAGGA
R:
CCTCTCCGATCCTAGCCTCTG
Band lengths:
347-1703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]