BtaINT0041731 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89162580-89163464:+
Coord C1 exon
chr12:89162580-89162771
Coord A exon
chr12:89162772-89163177
Coord C2 exon
chr12:89163178-89163464
Length
406 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
TCAGCCGCCTCCCTCCGCAGGGC
3' ss Score
10.98
Exon sequences
Seq C1 exon
GGGAGCCGGGCCGCCCCGGAAGCCCCGGCCTGCCCGGCATGCCCGGCCGAAGCATCAGCATCGGGTACCTCCTGGTGAAGCACAGCCAGACCGACAAGGAGCCCATGTGCCCCGTGGGCATGAACAAGCTCTGGAGCGGGTACAGTCTGCTCTACTTCGAGGGCCAGGAGAAGGCCCACAACCAGGACCTGG
Seq A exon
GTAGGTACCGCCCGCCAGCCGGCCAGCCCCACCGCGGGTGGCAGGACCCAGCGGCCAGTTACTTCCTGAGTCCCCCGAAGGCACCCGGATGCTCCAAACCCGGGGTCGGGACGGGGCACTGCCCTGTGTCCGGGGCCCTCTGTAAGGGCAGGGGGGAAGCGCCAGTGGAGGCCCCCAAGGGATCGGAGAGCCAGAGCTTGCCCCCTGCCCCGCCTCGTGCACGCTGAGCTCTTCGGGTGGCCAGGGCGTGGCCGGGCCCTGAGTGGGCGGGGCACCCGGGACCCCGCCTCCTCACACACTCAGCCGCCTTCCTCCGTTGGCCGGTGGCCGGGGCGTGGCAGGGCCCTGAGCGGGCCAGGCACCCGGGGCCCCTCCTCCGCGCACACTCAGCCGCCTCCCTCCGCAG
Seq C2 exon
GGCTGGCGGGCTCCTGCCTGGCACGGTTCAGCACCATGCCCTTCCTGTACTGCAACCCCGGGGACGTCTGCTACTATGCCAGCCGTAACGACAAGTCCTACTGGCTGTCCACCACCGCCCCGCTGCCCATGATGCCCGTGGCCGAGGAGGACATCCGGCCCTACATCAGCCGCTGCTCTGTGTGCGAGGCCCCGGCCGTCGCCATCGCAGTCCACAGCCAGGATGTCTCCATCCCCCACTGCCCGGCCGGGTGGCGCAGCTTGTGGATCGGATACTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210:ENSBTAT00000005916:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.246 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(38.2=32.3),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
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:
GGGCATGAACAAGCTCTGGAG
R:
GTATCCGATCCACAAGCTGCG
Band lengths:
352-758
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development