BtaINT0041730 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89161329-89162771:+
Coord C1 exon
chr12:89161329-89161445
Coord A exon
chr12:89161446-89162579
Coord C2 exon
chr12:89162580-89162771
Length
1134 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GCGGCCTCTGTCTCGCCCAGGGG
3' ss Score
6.65
Exon sequences
Seq C1 exon
GTTTCCGTGGGGCGCAGGGCAAGGCCGGGCCCCAGGGACGAGGCGGCGTGTCGGCCATTCCGGGATTCCGTGGAGACCAGGGGCCCGTGGGGCTGCAGGGACCGGTGGGCTTCGAAG
Seq A exon
GTGAGTGATGGGCAGGGGGCAGGGAGGTGCCTCAGCTCCGCCATGGGGCTGACAGGTGGACCGCGGAGCTCAGGGAGGGGTCGGACGAGCCCCGAGATGAGCAGCGCTGAGGGGCTGCCCCCGAGTCCGGCTCCCGGGTTATCAGGACCCACCCCGTGACCCCTGCCCCTGGCAGAGCATGTGGCACGGGGTCCCTGCCACAGGCTGGCCTCCTTCCTTCCCATGAGACATCAGGAGGTGGCTCAGAGAAGGAAGCGGGTGACGTGCTCTGAGAGACAGGATTCCTGAGCTCGCAAAAGCTGAGGACAATGAACTACAAGTGACCGATCACATTATAGGCACCACTGTGAAGCCTTTTATCGTCGACTTCTAAAAATTATCTGCATGCATGCAGGATGGGATAGGCCAGAAGTAGTAGCCATTCATGCAAAAAAAAAAAAAGTCCTGGGAGTTGTTGTAATTCACCTGCACTTGGTTTGAGCCAGTGACGTGAGTGCTGTGCACGGTAGAGATAGGCTGCATGGTCACACCCAGACCCCAGCAAGTGTCCACATCACGCCACTCGAGCAGGAGAGCCTGTGACGCGCGGGGGAGACACCACCTGAGACACGCATAGTGGGGGCTGGGGCGGGGGGCGAGGGGCGAGGGGCCGCCCCGTGAAAGAGGGTCACCAGCTGGAGGCGGATCGGCCGTTCTGCGGTATCAGGGGCAGAATTGGGGCCCTGGGTGGACACGTGGGGAGTCGGGTTTCTAACCCCAGGAACGGCCGCTCCCCGAAGGTCCAGCAGGGAGCCTGCAGCCTGGCACAGAGGAGGCGGGCAGGGCTGGACCGCAGTGCCCCTGGGCGCCTGCACAGTGGCAGACGCTGCAGTTCCCTCGAAGGAGGTGCCCGGGGGTCAGCTCAGGGGCCTCTGAGTCCACGGCCCCCCATCCAGCCCCTTCATGATAGCCATTCCACGTTCCTGAACGGGGCAGGGGGGATTAAGTGAGGGTAAGTCCTCGCCAGGAGGCTCTTGGTCCCCAAGGGCAGAGCCACTGACCCCAGCCTTGGGGACGTGAATGTCGCCGTGTGCGCCGCCAGCACGCGGGCTGCGGTCCGTGCAGCAGCTGCAAGGCGGCCTCTGTCTCGCCCAG
Seq C2 exon
GGGAGCCGGGCCGCCCCGGAAGCCCCGGCCTGCCCGGCATGCCCGGCCGAAGCATCAGCATCGGGTACCTCCTGGTGAAGCACAGCCAGACCGACAAGGAGCCCATGTGCCCCGTGGGCATGAACAAGCTCTGGAGCGGGTACAGTCTGCTCTACTTCGAGGGCCAGGAGAAGGCCCACAACCAGGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210:ENSBTAT00000005916:42
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.246
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(41.2=52.5),PF0139113=Collagen=PU(60.0=82.5)
A:
NA
C2:
PF0139113=Collagen=PD(38.2=32.3),PF0141314=C4=PU(39.8=66.2)
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:
GGGATTCCGTGGAGACCAGG
R:
CAGGTCCTGGTTGTGGGC
Band lengths:
247-1381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development