BtaINT0039284 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015085 | CLIC3
Description
Bos taurus chloride intracellular channel 3 (CLIC3), mRNA. [Source:RefSeq mRNA;Acc:NM_001100301]
Coordinates
chr11:106230413-106233455:+
Coord C1 exon
chr11:106230413-106230588
Coord A exon
chr11:106230589-106230671
Coord C2 exon
chr11:106230672-106233455
Length
83 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGC
5' ss Score
6.06
3' ss Seq
ACGGCGCCCCTCGCCCGCAGACG
3' ss Score
10.59
Exon sequences
Seq C1 exon
CTCTGTACCAGCAGCTGCTGCGCGCCCTCGCCAAGCTGGACAGCTACCTGCGCGCGCCCCTGGAGCACGAGCTGGGCCGCGAGCCGCAGCTGCGCGAGTCCCGCCGCCGCTTTCTGGACGGCGATCAGCTCACGCTGGCCGACTGCGGCCTGCTGCCCAAGCTGCACGTCGTGAAC
Seq A exon
GTGAGCGCCGGGGCGGGGCGGGGCGGGGCGGCGCGGGGCGGGCAGACCCGCCAGGAGACCCTGACGGCGCCCCTCGCCCGCAG
Seq C2 exon
ACGGTGTGCGCGCACTTCCGCCAAGCTCCCATCCCCGCTGAGCTGCGCGGCCTCCGCCGCTACTTGGACTGCGCCCTGCAGGAGAAGGAGTTCAAGTACACGTGTCCCCACAGCGCCGAGATCCTGGCGGCGTACCGGCCCGTCGTGCGCCCCCGCTAGCGCCCCCCGCCACCTGCCCACTCGTCTGCAGCCCCATAAAGGCACCTCTGCCCCAGTGAGCGCGAAGGGGCATCGGAGGGACCAGAGGCCCTCAGTTTCTGCCACTACCGAACGCCCACCCTGGGCCGCTCAACTCCAGACAACAGCCCACGAGGACAGACAAGAGAAGCCGGTGGGCGGGGTGCGGTCCATCTCCCTACTCCTCGGGGATGGCAGGACTGGATTGGGCTCCCAAACCAGTCAGGCCAGGGTGGGGCGGCAGGATGGCTGGGGAGGGTGGAGAGCGAAGCCCCGTCTGGGCAACTCCGGGCCAGAGGGCGGGCCCCACATTCTTCAGCTCTGCCCAGGCGCAGACAGACCACCCCCCACCTCCCTGGCCATCGTGTGGGGTCTGCATCACTGAGGCATGTGCCCGCTGGGGCGGGAACAAGGTTTCTAGCCTCTCAGAGCCCCACCCTTGCACAGCCGGCTGGGCTCCTGGGCGTGCCGAGCAGGGACAGGTGGGCAGGGCTAGAGAGGTGGGCAGTCTCACCAGGAAACGCAGAGCCTGACACGGCCCCATGCCCAGCCCGCGGGCCCGGGAGCCAGCGTCTGGCCATGACCTCATGACTTTCGCCAGATGAAGCTGTTTATTTGACGGGGAAGGGGCTAGAGGAGTGGCCTTGTTCGGCCTGGCAGCAGGCTGGGCAGGTGCCGGCAGGAGGTCCTGGGGGCCGCCCCTGCCCTCTCCTCGCAGGCACAGTCCTGACGTCACACTTTCCGTGGTGCCTTCAGGGGTCATCAAAGTCTACACCACTTGCCGGCTTCTTACTGGGAGAGAAGAGGGGATGACGCTGTGGGGTGTGGAGGGGTGGGCAGGGTCCATGCTGGACCCTGGGCACAGGAGGGATGGGGGGCGGGGAGGCACCTCTTGAAGCCGGGGTTGATGAGAGACTCCCCTGGACACCGCCTCTTGACCCCAGGTCCGGGGCCACCTCTCTGAGGATCTGGGTCTGGGGAAACAGGAGGGGGGGGCTGAGTCCAGCAAGACCCCAGGCCCACGACCCCCCTACCACAAGGACAGAGCCTCTCTCTGGACTTTAAGGCTTGTTCTTGAGTTCCAGCACAGTCAGTGCGGCCCCAACCCGAGTCACAAGTGACAGGCCTTACCTGGTAAGAAGAGACGAGGCCCCGCCTGCCGGGCGCTCTTCCTGGGGCTGGTGGCCGTCTCCTCCGCTGCAGCAGCTGGGGGGTGGAAAGCAGGAATGCAGGCCCGGCCTGGGGGACCTTAGTGAGCCCAGGTGGGGGGTTCCCACCCCCACCTACCTGCCAGCCGCCGCTCCAAGCTGCACACACGCTCCGCCAAGCCCAGTGTCAGTGTCTGCAACCTGGAGGCTGCCTCTGGGCCCGGCACCTTGGACAGGTCAAGTTCCAGCGCCGAGGGGCCCCCTGAAAGGGTCAGGGACGCTCTGTCTTCCTGCAGGGTGAGAGTCACAGCTTGCTGCTCGCAGGCTGCCCTGGGGAAGGAGGGGGGCTGAGTACCGTGGCCACATCCACTGCTCCCCACCCACCCTGCCTCTCTGCTCAGAGGCTCACCTGAATCGGAGGGCGATGTCTTCAGCCGCACTGAGGCCAAAACGGGCTTTCTACAGGGCACAAGGGCTGGTCATCAGGGGCCTGAGACCCTACAGTCTCTGGGGACACCCTCAATCCGCAAGACCAGGCCTCCTGGGGCAGCTGCAGGGCCGTGGGAAGGGTGCCCAGGTACTTCCGGGAAATTCCAGGCCGCCCCCTGCGAGCCCACAGGCGGTCCGCGCTGCAGGTGTGTGGTGCGGGGGGCCTCCCGGCCACCCAGGAGCCCCGTTACCCACCAGGGCCGCCAGGCGGTCCGGCGTGAAGCAGGTGCTCCAGAGCTCCGCGGCGTCCGTCACACTGCGGGGCAGGGGCAGTCAGGCCGAGCCGCCCGCGCCCCCTCGCAGCCCCGCGGGACCCGCTACTCACCAGAGGTTGAAGCCGCCGCGTTCCCCGGGCCCGCCGCCCTCCCCCTCGCAGTAGCACACGAAGCGCGGGGGTCCGGGGCCCGGCGGCAGCGTGCAGAGAGGCGGCGGCACCATGGCGCCTCGGCGGGCGGAGGGATCCGGCGGGCAGGGCTCCGCGGCTGGGGCGCCTGCGGGCCCGGGGCGCCCGCCGATCTGCGGCGCCTCGGGACCTGGGGCGCCTGCGCGGGCAAAAGGCTTCCGGATCGGGGCGGGTGGGGCGGGGCTTAGCCCGGGGCGGAGCCTGCACCGTAGGGCGGGGCTTAGTCCGGGGCGGAGCCTGCGCCGTGGGGCAGGGCCGCAAGCACGGCTCGGGCTACCAGGCTCCTCTCACCGAATCTAGTCACCGTCTGGGGCTTGGCCCCCGGCGCACACTTGGGGGCCTCTTTGGACCTTCCCTTCTGCGCGCCCCCTGTCCCCGCTGAGTCCGGGGTTCCCCCCTTGGCGCAAGCCCTGAGGGGGCGCAGGCCTCTCCAGCCACCACTTTGGGCTCAGATCTCTTTGACCCCCCTTCTCTGGTCCCTGCGGCCTCCCCCTAGCCTCCGCACCCCTCTTCCTGTGTCAACTGGAACAAGTCAAATACAAAACAGAATAAAGTATGGTAACCCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015085:ENSBTAT00000020075:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134101=GST_C_2=FE(44.3=100)
A:
NA
C2:
PF134101=GST_C_2=PD(17.6=43.4)
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:
GCTTTCTGGACGGCGATCAG
R:
TGGGGACACGTGTACTTGAAC
Band lengths:
178-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development