BtaINT0039279 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010948 | CLIC2
Description
Bos taurus chloride intracellular channel 2 (CLIC2), mRNA. [Source:RefSeq mRNA;Acc:NM_001081727]
Coordinates
chrX:38520875-38523525:+
Coord C1 exon
chrX:38520875-38521056
Coord A exon
chrX:38521057-38521664
Coord C2 exon
chrX:38521665-38523525
Length
608 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TTTTTTTCCCAAAACCCTAGGTT
3' ss Score
8.79
Exon sequences
Seq C1 exon
CCTTTGAAAAATCTCTGCTTAAGGAATTTAAGCGTCTGGATGACTATTTGAACACCCCACTTCTGGATGAAATTGATCCAGACAGTACTGAGGAACTCACAGTCTCCAGAAGATTGTTCTTGGATGGCGATCAACTGACCCTGGCTGACTGTAGTTTGTTACCCAAACTGCACATTATTAAA
Seq A exon
GTAAGTCTTTACAGGGTGGGCTGAATGATTGAGAAGGGTCTGGGGAGTCGCCAGCAGGAAGCACAGTGACCATTCAGTGTGAGGTTTTTATATTATTGATTTTTCATCATTGTTATGCATAGTGTATGTCTCCTTTCCTCCTCAGAGGAAAAATCCATAATGATCTCCACTGGAAAACATAAACACTTCTTGCTTCTTTCTTCCTAAATCAGAAGGTGTTTTCCTACTGTCTTGTCTATAAAACAAGGGTACCTATTGCACAGAATTGTTGAGGAGTAAGACACTGTTGGAACCCTAAACAAACTCTTAGTCCAGTAAAGAGATACAAGCTCTTTATCTGTGCTTCCTTCTTCTAAATATATTTATAATTAAATATAGCATAAATATAAAAATAATTACAAACATGACGTTTTGTTTACATATGTAGAAAAAGAACATTAAAGTAGTAAATCCAAGATTCTTTAAGTTTATTTTGTACTTTTTGTGTAGATAATATGTCCTCAATGATCTGGACCTTTGAGATATATTTTTACACAGTTGGCATGTTACTGATGCCCCTCACTACCAACTGCTTTTCCTCTTTTTTTTTTTTTTTCCCAAAACCCTAG
Seq C2 exon
GTTGCTGCAAAGAAATACCGTGACTTTGACATTCCAGTAGAATTCTCAGGAGTCTGGCGCTATCTCCACAATGCCTATGCCCGTGAAGAATTTACCCACACATGTCCAGAAGACAAAGAAATTGAAAATACCTATGCAAGTGTGGCTAAACAGAAGAGTTAGGACAGCCCTTTCAGTAGAAAAATCTCTCTTTTCACTTGCTATCATACTAGAAAGTCTTTTAGAAATAAGAATATGGAAAATGCTGTTTCCTCTATTCAACTTTCTTATGAAAAAGAATACTGTATTTTCTGTACCTAGTTAATCCAAACTATCTGCTTACTGTGTATTTTACAGGTCTTCATATTTCATTTTTTAATTCCCATGGCACAACCACTGCAATTTTAAATTATATGAAAAGTGTCAATATCTTTTACCATTTGATTGAAATCCTAGAAGGTATCATGTGTGCAAGCTCAACCGATGGCTAAAGTTACAAATGACATATAGTCATGGTTTCAAACTGTCCCTTAGAGACATTTCCACCTAAATCATTAAAACAATTTTACTAAGACATCTGACTGACCAAAAGGTCTTCTTGCTATTCACTAAAGGGTAAAGTAAACCATTCTTAGAGAATAATCATAAATTTTTCTACAGAATTTTAAACTGTTCCATTATTAAATGTACTCAGATGTCCACCTTAAAATGCAATCAAATCACTCAAATCTGAAAACAAAAACTGAACTTTACTCATGGTCCTTCAGAGAAGAAACAAAGTTTAGCTTCAAAAAAGAAATACAGGTGCTATTATACGTCTTGGTGGGAGTTAGATAAAATTTATTTATTTATGGCCAACCCCAGGGCATGTGGGATCTCAGTTCAGTTCCCCAACCAGGGATGGAAACCATGCCCCTTACAGTGGAAGTGCTGAGTCTTCACCACTAGGGAATTCCCTAGAAAAAAATCTCAATGAAGCAGTGTTTTAATAGGTTCAAACAAAAGTAAGGCAATGAGTACAGAGTTAACAGGTACATGAAATAGGCGCATGAAAAGATGCTCACTATCGCCAATTATTAGAGAAATACAAATCAAAACTGCAGTGAGGTACCAGCCCACACTGGTCAGAATGACCATCATTTAAAAGTCTACAAATAACAAATGCTGGATAGGGTGTGGAGAAAAGAGAACCCTCCTACACTGCTGGTGGGAATGTAAACTTGTGTAGCCACTACAGAGAACAGTATGGAGGTTCCTCAAAAAACTAAAAATGGAGCTACCATATGACCCTGCAATCCAATTCCTGGGCATATATTTAGAACTATAATTTGAAAAGATACATCCACCCATATGTTCATAGCAGCATTATTTACAATAGCCAAGACACTGAAACAGCCTAAATGTCCATCAACAGATGAATGGATAAAGAAGATATGATATGTGTGTGTGTGTGTGTGTGTGTGGTATGCTAAGTTGCTTCAGTCGTGTCTGACCCTTTGTGACCCTATGGACTGTAGCCTGCCAGGCTTCTCGCTCCATGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGTCATGCCCTCCTCCGGGGGGTCTTCCCGACCCAGGAATCGAACATGACTCTTTTATGTTTCTTGCATTGGCAGGTGGGTTCTTTACCAGTAGTGCCACATGGGATGGCCTTGACACATGCACACTACTATATATAAAATAACTATAAAGACCTACTGTACAAGAAACTCAACTTAATACTCAGTAAAGACCTATATGGGGAAAGAATCCAAAAAAAGAGTGAATATATGTATAACTGATTCACTTTGCTGTACACCTGAAACTAACAAATCATTGTATACTAAATATACTCCAATAAAAATTAATTATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010948:ENSBTAT00000014537:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF134101=GST_C_2=FE(41.7=100)
A:
NA
C2:
PF134101=GST_C_2=PD(16.0=42.6)
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:
AGGAATTTAAGCGTCTGGATGACT
R:
TTTCTACTGAAAGGGCTGTCC
Band lengths:
343-951
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]