BtaINT0039274 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013533 | CLIC1
Description
Bos taurus chloride intracellular channel 1 (CLIC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001015608]
Coordinates
chr23:27397095-27398934:+
Coord C1 exon
chr23:27397095-27397276
Coord A exon
chr23:27397277-27398542
Coord C2 exon
chr23:27398543-27398934
Length
1266 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCTCCTTCCCGCACCCCTAGGTG
3' ss Score
11.73
Exon sequences
Seq C1 exon
ACCTGGAGAAGGGGCTCCTGAAAGCCCTGAAAGTATTAGACAATTACCTGACATCCCCCCTCCCAGATGAAGTAGATGAGACCAGTGCTGAGGATGAGGGGATCTCTCAGAGGAAATTTCTGGATGGCAATGAGCTCACTCTGGCTGACTGCAATCTGTTGCCCAAGCTCCACATAGTACAG
Seq A exon
GTGAGTAGTGATTGTGGGAGGAGTAGGTGGGAGGTGGGATGACTCTTTAAGGGGCTCCCATGCAGGCTTCTCATGACAACCACTCCAAAGGTGGTTTCTTTCTGAGTAGTTTCCAATGGCAGACACCACCCTATTCCTTCTCTGCTATCTTTGCTGGCAAGACCACTGGTTGGGAGAATTAATTACATTCCACCATGCAAGGTGTGGGTGCAAACAGACTGAGAGTAACACATCCCAGTACTGCTTTCAAGAATGCTCTTCCTGTCTCTATCATTGCCAAATCCCCAGATCAGACAGACCAGGCTTTTCCTAAAATCAAAGTTTTAAGTCTGTTGTTTCAGTCTCCACTTATCTTCCTCTTGTGGAAGATGAAAAGTGCTGGTTCCCTTGTTTTTGTCACAGCTCAAAGCTATGGTTTAGTTTGTGAAACGTGAGCCCGGTGTCAGTCTGCTGCAGAACTGTGTATTGAAAATCTCTGTATTTATTTATTTGGCTGCACAGAGCCTTAGCTGTAGCATGAGGGACCTTTGATCTTGGCATGCTGCAGGTAAGTCCCTGCCTGCAAAGGATTTGAAATCTAGCTGAGAAAATAACTTTCACATGAAAGTTAATAATACATGATTAAAAGCCAAATGACAAGTAGACAGAAATTGCTGTGGAAATTTAAGAGAACTTTATGGTTTGTGAATTATATCTCAAAATTAGGACGAGAAAACAAGCACCATGGACTGGGGTGGTCTGAAAGGGGCTGGTTATAAATGGCCAGGATTTCAGTAAGTGGAGAGAAAGGGTGAAGGCCTTACCAGACAGGAGTTAAGATGACTGCAGGTGATTATGTGGGAGATGAGTCATAAGGACTGATGTTGAAGCTGAAACTCCAGTACTTAGGCCACCTGATGCAAAGAGCTGACTTATTTGAAAAGATCCTGATGCTGGGAAAGATTGAAGGCAGGAGGAGAAGGGGACCAACACAGGATAAGGTGGTTGGATGGCATCACCAACTCAATAGCCATGAGTTTGGGTAAACTCAGGGAGTTGGTGATGGACAGGGAGGCCTGGCGTGCTGCAGTCCATGGAGTCGCAAAGAGTTGGGACTGAGTGACTGAACTGAACTGATGAGTCATAAGAAAAGAAACCAGGTATCGAACTTGCTTAAATGCCTGGATTTTATCATATAGGCTTTGGGATAAGGGAAGGACCAAGGGCATGGCAGCTGGTGTGACTTTCCTGAGGCTAACCTATGGGTCCTCCTTCCCGCACCCCTAG
Seq C2 exon
GTGGTATGTAAGAAGTACCGGGGATTCTCCATTCCGGATGTGTTTCGTGGAGTGCATCGATACCTGCGCAATGCCTATGCTAGGGAAGAGTTTGCTTCCACCTGTCCAGATGATGAGGAAATCGAGCTGGCCTATGAGCAAGTGGCCAAGGCCCTCAAATAAGGCCCTTCCTAGGGCCACCCGACCCCCCCTCCATTTTCTTCACAAAGGCCCTGGGTGGTTTCCACATGCTACCCAACGGACACACTCAAAATGGCCAGTGGGCGTAGAATCCTGAAGCACCTGTGCAGGGCTTGCTGGGGGCGATGAGAAGCAAGGATGGGGGATCTTCGAGAGATTTTTATTGTGGGGTGGGTTGGACAATGTATTTCAGTAATAAAATACAGAATGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013533:ENSBTAT00000017995:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134101=GST_C_2=FE(66.7=100)
A:
NA
C2:
PF134101=GST_C_2=PD(25.6=42.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATCTGTTGCCCAAGCTCCA
R:
TCCCCCATCCTTGCTTCTCAT
Band lengths:
357-1623
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]