BtaINT0039289 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009470 | CLIC4
Description
Bos taurus chloride intracellular channel 4 (CLIC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001080218]
Coordinates
chr2:128710453-128712376:-
Coord C1 exon
chr2:128712195-128712376
Coord A exon
chr2:128711016-128712194
Coord C2 exon
chr2:128710453-128711015
Length
1179 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TTGATCTCTTTGTATTTTAGGTG
3' ss Score
12.03
Exon sequences
Seq C1 exon
CTTTGGAGCGAGGTCTCTTGAAAACACTGCAGAAACTAGATGAATATCTGAATTCTCCCCTCCCTGATGAAATTGATGAGAATAGTATGGAGGACATTAAGTTTTCCACACGTAAATTTCTGGATGGCAATGAAATGACACTAGCTGACTGCAACCTGCTGCCCAAGCTGCACATTGTCAAG
Seq A exon
GTAGGCCTGCAGGATGTGGGTCACGTTGCTCTTAAACCTGATACCTTTTTACAAAGACAGGACTCCCCCTGTGTGTAAAACTTGACTGGTATTCTGACACTCACTATTTAGAACCTCCAAACAGTGTAACTTAATGTTGTCTAGGCAATAGGTGAAACACCCTAAGGTGTATTAAATGGAAAATTGTGTATTAAAATCAATGCCTATGAGAAATGGAAAAAATTTTTTTCTGTGACTGCATAAAAATTCAAGGTAACTTTAAAGTGCTTGCTACACTTACATACAGCATCAAACTTTGTTCTTTGATCACCTGGCTTTTTCTTTTCAAGGCAGAAAATATTTACTGAGCATTTATTGTGTGACTACATTTACTGGGTTTCCCAGGTAACACTAGTGGGGAGACATAAGAGACATGGGTTCGATCCCTGAGTTGGGAAGATCCCCTGGAGGAGGGCACAGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCTATGGACAGAGGAGCCTGGCGGGCTGTGGTCCATAGGGTCACAAAGAGTCGGACTCGACTGAGCGGCTAACACAAGTGACAGTGTGTGAAACACTGTGCTGTGCACTAAAGATCAAGGTCAAGAAAAACAGGTCTCGACTAGTGTGTATGTTTGCAGCGATATCTTTTCAATCCATCTCTCAGAATAATGGAAATAAAAACAAGAATAAACAAATGGGACCTACCTAAACTCAAAAACTTTTGCACAGCAAAGGAAACAAACAAAATGAAGAGACAACCCACAGATTGGGAGAAAATATTTGCAAACGATGTGACTGACAGGAGATTAGTCTCCAAAATTTACAAACATCTCATGATTTTTAACAACATCAAAACAACCCAATCAAAAAATGGACCAAAGACCTAAACTATTGTGTATGTTTTAAAGTATTTATCCAGTGATTGCACTTGACTGTTTCTCTTGTTGGTAAAGGCAGGCGTTTGCAGTCACCACCACACTTCTGAATTTCTGGTGTGGTTTGCGGTCCTTATCATTATTTTAAATGTCTAGTTATAATGAAGGGGACAGACTTCAAGTAGAGGCAGTTTTGAGAGGTTCATGGAATTAATTTGCCCTAAAATCAGATACATGTCTGGTTTGTAAGACATGGCATATAAACATTAACTTTTGATCTCTTTGTATTTTAG
Seq C2 exon
GTGGTGGCAAAAAAATACCGCAACTTCGATATTCCAAAAGGAATGACTGGCATCTGGAGATACCTAACTAATGCCTACAGTAGGGATGAGTTCACCAACACCTGCCCCAGTGATAAGGAGGTTGAAATAGCATACAGTGATGTAGCCAAGAGACTTACCAAATAAAAGAGCACTTATGAGAGAAGCGTCTTCACATCTTCCCCTGACTAAGAACATACTTTCCCTAACAGACTGCTCCTCTTCCTAGAAAGTAGAAACTTTATTTGGCACGAACATGCAGTTATTCCAGATTAGGATAAAGGATAGACAAGGTATAGTAGCTCTCTCGAAATATATATACTCCTAAGCAGTATTATTTTAAAATTCATTTACCCTGCCTATATCCCCTAGCCTGTATCCTCCTCTCCTCCAATTTGGAGACACTCCATCACAAACTTTCACTTTAACGGTAGTTTAAAGGTAGTTTGCCATCTCTCTGGAGCCTTCATCCCTGGAGTCCATTCACTGTGTATCGATGACAGAACTTTTGAGGTGCACTGTTCAACTGTTAAAATAGTAACCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009470:ENSBTAT00000054397:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134101=GST_C_2=FE(58.3=100)
A:
NA
C2:
PF134101=GST_C_2=PD(22.3=41.8)
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:
ATCTGAATTCTCCCCTCCCTGA
R:
CAGGGGAAGATGTGAAGACGC
Band lengths:
342-1521
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]