BtaINT0041414 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013183 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:22990]
Coordinates
chr7:40675390-40676263:-
Coord C1 exon
chr7:40676225-40676263
Coord A exon
chr7:40675785-40676224
Coord C2 exon
chr7:40675390-40675784
Length
440 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
GTCTTTCCCTCCTTTTCTAGTGA
3' ss Score
10.79
Exon sequences
Seq C1 exon
GGCCCCGATGGACTGCCTGTGCCTGGCTGCTGGCATAAG
Seq A exon
GTAACTTTCAGGGAAGAGTCTCCAAGGCAGGCTAGGAGGAGTGGGAGAGCCAAGGGAACCCTGGGGCTGAGTGCCTGCCGCTCCCTACATCGTGATGGAACAGCCAGGTCTCCCCAAGTAACCCTAGATTTGACTCTCCCATCGTGTGGCCCAAGACCCAGGGCTGTGATCCTGGTTGTGAGCAAACCACCCTCTTGGTCATACAGGGCTCACTCAAGCCCTGGCCCAGCCAGGGCAAAGCTATCAGCCCGTGAGACTTTGTTCATACTGTCCCTCCCCCACCCCAAGAGAGGGTGGAATTCAGGAGGTTAGGATGAGAGGATTGGGGGGCCATACCTCTGCCCAAGGAAATAGGCAGGACAGGGATACCCAGATCAGAAACAGGGCTTCTGGGCCCCCCCAGTTCCCTCCTCACCTTCAGTCTTTCCCTCCTTTTCTAG
Seq C2 exon
TGATCCTGAGCACGCAGTTCACAACCTGTATAGATCCATGTGGACATTTTTAATTTTTGTGAAAACAAAACAGTAATATATTGATCTATTTTCACGGGATGCAACACCAATACTTGTGGCCTTTTAACATCAGAGAGTGTGCCCAGCCCAGCCCCAGGACAATCAGTGTGTGAAGCTGGCAGGAAAGCGGACAGGCCCCCTGGGGGCACTGTGTACCTGCAGGGCTCCCTCGGGGCTTGGCTTTCCAGGAAGGAGATGAAAGTAACTTGCCTGGCTCAGGAGAGGCTGCAGAGAGGCCAGGTTGGGCTTTCGGTCACCTGAGAGCAGAAACTCCGGCTGCTCCACTGCCCTGCAAGAGCCTGCCCTCTGAAGCTCTGGAGCTCCGGGCCATGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013183:ENSBTAT00000017548:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.0=38.5)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGGACTGCCTGTGCCTG
R:
GCTCTCAGGTGACCGAAAGC
Band lengths:
358-798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]