BtaINT0073183 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005546 | HOXB7
Description
Bos taurus homeobox B7 (HOXB7), mRNA. [Source:RefSeq mRNA;Acc:NM_174342]
Coordinates
chr19:38518637-38521061:+
Coord C1 exon
chr19:38518637-38519055
Coord A exon
chr19:38519056-38520804
Coord C2 exon
chr19:38520805-38521061
Length
1749 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACG
5' ss Score
10.52
3' ss Seq
CCCGTAAATACTCTGCGCAGGGA
3' ss Score
5.14
Exon sequences
Seq C1 exon
CAAATCATCCGGCCAAATTATGAGTTCATTGTATTATGCGAATGCTTTATTTTCTAAATATCCTGCCGCAAGTTCGGTTTTCGCTACCGGAGCCTTCCCCGAACAAACTTCTTGTGCGTTTGCTTCCAACCCCCAGCGCCCGGGCTATGGAGCCGGTTCGGGCGCTTCCTTCGCCGCCTCGATGCAGGGCTTGTACCCCGGCGGGGGGGGCATGGCGGGCCAGAGCGCAGCCGGCGTCTACGCGGCCGGCTACGGGCTCGAGCCGAGTTCCTTCAACATGCACTGCGCGCCCTTTGAGCAGAACCTCTCCGGGGTGTGTCCCGGCGACTCTGCCAAGGCGGCGGGCGCCAAGGAGCAGAGGGACTCGGACTTGGCGGCCGAGAGTAACTTCCGGATCTACCCCTGGATGCGAAGCTCAG
Seq A exon
GTAACGCCGCGCACCGAGCCGTCCCGAGCCGCAGTGGCCCGGGCACATATCCCGGAAGGCGCCCCCTTCCCGGCCAACCGCCCTTCTTCGCGTCCAGAGTGCTCCTGGTAGGAGATCGGCCCTGGGGACGCGGCCCCCCCTGAGCCGCGACACGGCGCGCCGCCCCCCTCCCATTTTTGCTTGGTGCTCTCAGGCTCGCTCTGCTTCCCTGGCGGATCCCTCTTCGCCGACGCCGCGGCGCTCTGAGCCCCCAGCCCACCCCCCACTCTTCCTCCTGGCCTTTTAGCTTTAAATATTTATCAGCCGCGCCGGCACGGGCTGGAGACGAGGCCGTTTGTCTTGCGGAGGAAGGCTGGGGTTTGCAGAGAATAGCCATTAGGGTCTCCCCCCCTCCCTTCACCCTTCCCCCGGCGGGGATCTCATCTCCGGGTGTGTCCCCTCAGCCCCAGCTTGGATGAGGTCTGGGGGAGGGGGCTGTAGCTCTGAGCGGTTCTCCCCTCCCTCTTTCCTCCCAGCCAACCCGCTCCCCCATTATTCCCTTCTGGACAATTAGAGGTGGGCTCTAGAGGCCTGGCGGGAGGAGGGGGTGTGAGAAGAGCTGAGGATTCAGTCAGGGACACAGAGGCAGGTGGAGAGAAGGGGGCGGAGGCCAAAAGAGAGAGGCTTCTGACTCCCCAGTGAACTTGGGAAGGGGGAGGCAGGAGAACTAGAGAATGGAGCAGAGGCCTCATGGGGAGCCCAGCTGACTTCCTCAGGTGCCCTTCCTAGCACCCCTGGAGAACTGGCCAACAAGTTTTCCAGTGTCCTTCCAGAAGGATGGATGTTCTCTTGGGGGAGAAACAAGGACTCCAAGAAGTCAAATCAAGAGTTAGAGAGTGCAGGCCGCTGAGGCAGCTACTGCAGAAACCCCAAGAGACCAGAGGCACTGTGGGGGTCTCCTGACAAGCCTGTCCCAGACAGCCTTCTTTGTGTTGCCCTGGACTCCAAGGCCTCTCTCAAGATCCAGGAAACCCAAGATATGTGGTCAGAGGCTCCCAGTCCAGCCAGGGTTGAGGGCCAAGAGAAGCCCAGCTCTTATTCCATCAGTATTAGTGGTCACAGTTCACATTACCTGCTCCATAATTCAACTGCCTTTCCAGCTGATTTATTAAAGCCCAAATTTTTCTGCTCATAAACATTTCAGCTTGGCTTTTATCTGACTTGAAATTAGGCCCCCAACCCCTCCTCCCACTGTCTCCTTCCTAGGAGGGCTGGCACCAGCACCTCCCCCAGCACAACCTCCCTCCAGCTTCCTCAGGGTTTGGGGCCTAACCTGGGAAGCTCTCCCCTGCCCATCTGCCCCCACCAGCCAGGTACTGAGTGTTCCACCCCAAACCAGGCTGCTGTCTCTCCTCTCCTCCTGTGCCTTCCCAGAGGCCCAAAGATTGCTTTGGAGGGCTGAGTTGTCTGGGCAGGTGGGCAGGCAGGACAGCCTGAACCTCAGCCACTCATTGGAAAGTAGCAGAGGGCAACTGCTCTCAGACCAACTCCACTGCGCCAAGGAAATCTGCAAATTCTCACCTCCTCCTCATTCCATAACAGGATGGGGGAGGGGGTAGACTGGACCTGTAAGGCGGTTTGTCTCCTTTTCTTTTTGCGAAAAGCCCTCAGGGCAGGCCTAGAGTCGCACTCCAGGGTCACTTGCATGGTTTTCCTTGTTATGGCTTATTCTGCACGCACTGACTTTTCTCCCGTAAATACTCTGCGCAG
Seq C2 exon
GGACCGACCGCAAGCGAGGACGCCAGACCTACACCCGCTATCAGACCCTGGAGCTGGAGAAGGAGTTTCACTACAATCGCTACCTGACGAGGCGGCGGCGCATCGAGATCGCGCACGCGCTCTGCCTCACAGAAAGACAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAAGAGAACAAGACCTCAGGCCCCGGGGCCGCCAGCCAGGACAAGGCCGAGATGGAGGAGGATGAGGAAGAGTGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005546:ENSBTAT00000007292:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.112 A=NA C2=0.369
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=67.1)
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:
CTTGTGCGTTTGCTTCCAACC
R:
TGATAGCGGGTGTAGGTCTGG
Band lengths:
352-2101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development