BtaINT0032421 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008723 | CCBE1
Description
collagen and calcium binding EGF domains 1 [Source:HGNC Symbol;Acc:HGNC:29426]
Coordinates
chr24:58886144-58887322:-
Coord C1 exon
chr24:58887287-58887322
Coord A exon
chr24:58886388-58887286
Coord C2 exon
chr24:58886144-58886387
Length
899 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
GACTCTTCTCTCCTGTGCAGGGA
3' ss Score
10.36
Exon sequences
Seq C1 exon
GGGGAAAGAGGCGCACCAGGCCCCAGAGGGTCTCCA
Seq A exon
GTAAGTAGCCCCACCTGTCTTGCTTCCCCAGGGCGGCGCGCTCGGGGCTCCCTCTCGGGGGAGCCTTCCTAGTTGGTTTGTTAACAATAGCCGGCCCCTTGCAGCTGTGGCTCAGCCTGGCCACAGGTAGCTTCGTGGTTACAGGAAGAGTCACAAGAGCCTTTTGCACCTGGTTGGGTTTTAAAAATCCACTTCCTGGTTTTGTTTGTTTTTGTCATGGCTAATCTTTATTTGAGCTTCCCTGGTGGCTCATCGGTAAAGAATCCACCTGCCAATGCAGGAGACGTGGGTTTGATCCCTCGGTTTGGAAGACCCCCTGGAGAAAGGGAATGGCTCCTGTGTTCTTGCCTGGAGAATTCCATGGACAGCGGAACCTAGCGGGCTACAGTCCATGGGATCGCCAAAGACTTGGACATGACTTAGCGACTAAACAGCAATGATGACAATCTTTATTTGGAATGTCTTCTCTTAAGATTCCAAACCCTAGCATGTCCTAAGTCTGTTTCCAGGTGTATCTTACAACATCCGAAGTGGCAGAGCTGAGGTTCAAATCCAAGAGAAGCCCAGCCTCTTAACCACTGCTCTGCGCCTCCTAGGGTTCTTTGGAAGGTAACCTAGGAGGGGTATTCTCAGATTTCGTCATTCTACCAGATTTGACGGAGTCTGAGAGCTAGGAGAGGTCCGTGTGCCACCACAGCGCATCTGGGAGGTGGAGGGGCACAGGGCGGCATCCGCCAGCTGTTGTTCATGGGCCTGATGTTTCCCCCGTTTGAGACACAGAGTTGGCGAGGTGGTCGCCAGCACATGGCAGGGCGGCCGGCCACGGCACCTCCGGGAGCCCTGGGTCAGCCATGGGGCGGGTCTCTGGTCGTCTGGTTTGACTCTTCTCTCCTGTGCAG
Seq C2 exon
GGACCCCCTGGTTCTTTCGATTTCCTGCTGATCGTGCTGGCGGAAATCCGTAATGACATCACCGAACTGCAGGAACAGGTGTTTGGGCGCCGGACTCACTCTTCGGCAGAGGAGTCCCCGTCACCGCAGGAACTTCCCAGCTATCCAGAGACCCTGGACATGGGCTCTGGAGATGACGCCCCCGGAAGAACTGAGACAAGAGCCTCCGGAGCCGCCAGAGACTTCTATCCTTAGCGCATCCCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008723:ENSBTAT00000011491:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.948
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.8=6.4)
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:
GGAAAGAGGCGCACCAGG
R:
GTGGGATGCGCTAAGGATAGA
Band lengths:
278-1177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]