BtaINT0065998 @ bosTau6
Intron Retention
Gene
ENSBTAG00000032288 | GCK
Description
Bos taurus glucokinase (hexokinase 4) (GCK), mRNA. [Source:RefSeq mRNA;Acc:NM_001102302]
Coordinates
chr4:77855557-77857151:+
Coord C1 exon
chr4:77855557-77855790
Coord A exon
chr4:77855791-77856040
Coord C2 exon
chr4:77856041-77857151
Length
250 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
CAAGCTTCCCCTCTACGCAGCTT
3' ss Score
6.74
Exon sequences
Seq C1 exon
CGATTCCGGTGACCGCAAGCAGATCTACAATATCCTGAGCACTCTAGGGCTGCGACCCTCGGCCACTGACTGTGACATCGTGCGCCGAGCCTGCGAGAGCGTGTCCACGCGCGCCGCGCACATGTGCGCCGCGGGACTGGCGGGCGTCATCAACCGGATGCGCGAAAGCCGCAGCGAGGACGTGATGCGCATCACCGTGGGCGTGGACGGCTCCGTGTACAAGCTGCACCCTAG
Seq A exon
GTGAGCCCGCGCGGCCTTCTGCCGGTCCAACCCTGGTCCAGCCTGCCCCTTGTGAGTTTGCATCCTTAGGGGAGAACCCGGGCGTTGGTCTCTATCTATGATACTCAGAGAGGGAAGCTCTCCGAGGTCCCGAGAACTCTTAAACTCTCCGAACTCCCTTGGCCCCCAGACACAGGAGGAGGGTTCCCTTGTTTTACCCCCTGCCGTGCATTCAGCGCGGTACCGGCAGCCAAGCTTCCCCTCTACGCAG
Seq C2 exon
CTTCAAGGAGCGGTTCCACGCCATCGTGCGCAGGCTGACGCCCAGCTGTGAAATCACCTTCATTGAGTCGGAGGAGGGCAGCGGCCGGGGCGCGGCCTTGATCTCCGCGGTGGCCTGTAAGAAGGCCTGCATGCTGGGCCAGTAAGAAGAAAGGCTGCAAGGCAGGAAGGAAGCTGTGGCCGGCTACTGGACCTGGGCTCCAGGGGACACTCTCCTTACAAGTCCCCCCAACCTGGCCCAATCGAGAGGCTTCTCCTTCTGAGGACCTTGGATGCCTCCCATCCCAGCTGTCACCTCCAGAAGATGGGGGAAAGCCTCTGGAGAGGTTGCCGAGGGCCCAGGCAGGCTTTTTCTCTCAGGGTCAGTTGGTGAGATAGCCCTAGGGCCCTGACTGGGTCGGGAGCAGAAATGAACAGGAATGCAGAACCCTCAAAGTACCTCGCCTTTTTTGCTGGAATCAAGGACCCAGAAGGGAGTTATTCACTCAGGATTTTGTTGCATTTCTGCACTGCTTGTCTCTTGGAGCTTTCAGCCTGGCTCAACCCTGGCTCTGAGAAGGGGGTGCCCTCTGGACCCTACTATGGCCTGGCTTCCCCATGAGCTCAGCCTGCATGGGGAGGCAGCCCTCATCACCTGGCCAGACCTAGACCTGGATTCCACAGGGGCCCCGGGGAGCTGCTGATCACTCAGGCCCGGGAAATGGAAGGGACAAGCTCCACAGTAGAGCCTGTGGGTACCCCGAGGCCTGGAGATGGCAGCCTTTTCCCTCCCATCCTGCCATCCCTGAGTGGTCTGTTGTTCTGGGATGGACCCTCACAGGAAATGCAGGAGACAGAGTCCCCAAAGCCTCTGCCCAGAGGGGCCCAGGAAAAGGAGGAGTCCCCCCACCCACAGACAGGCCTGGGAACATCTCTGGGATTGAGTCCCTGGCTCCCATGGCCCTGGGCACTCAGAAAGCCCAGCAGCACACAGCACACACCCCAAGGGACAAGCTAGGCCTCTTTCTTCTTAGCAGACTTCCATGTACCACACCAGCATATCCATGCCCAACCTGGAACTGTGTGGGGTTTTTTTTTTTTTTTAATTAAAAGTTTTAAAAGTTTAGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000032288:ENSBTAT00000045734:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0372711=Hexokinase_2=FE(32.5=100)
A:
NA
C2:
PF0372711=Hexokinase_2=PD(16.7=81.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTACAAGCTGCACCCTAG
R:
AGGCATCCAAGGTCCTCAGAA
Band lengths:
298-548
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]