BtaINT0041715 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89148921-89150723:+
Coord C1 exon
chr12:89148921-89149064
Coord A exon
chr12:89149065-89150600
Coord C2 exon
chr12:89150601-89150723
Length
1536 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CGCATTCTACTCCCTTCCAGGCA
3' ss Score
8.79
Exon sequences
Seq C1 exon
GGGCCAGGGGCTCCCCCGGGATGGACGGCTTTGAAGGCATGCTCGGCCTCAAGGGCAGACCTGGGCTCCCAGGAATCAAAGGAGAGGCAGGGTTTTTCGGAATTCCAGGGCTGAAGGGCCTGGCTGGTGAGCCGGGTGTGAAAG
Seq A exon
GTATGTCCCCTCTCAGCCAGACTGAGACTCCCTTTCAGCGGGGCCGACACTGCTCAGAACAGTGTCCCAGGAACCCACACACTAGACACCATTACAGAAGAAACTAGCTCCAGGAACTTGGTCCCTGCCACAGCGCACTGGCCGTGTAATAAGGGAGTGCCCCTAGCCGAAGGACACTTGAGAACCAAACTGACCCGGCTTTAAGAACCAAAACATCCTGAGAAATGCACCCCAGGTATATTCTGAAGGGCAGGAAGCACCTTTGGTGAAAGAGGGACACGGCAGTCCAGGTGGACAGATCCACTCCATGCAGAGAGACGGTGACCCCCAGGAGGGAGCCTGGACCAAGCTCCGGGCCCACCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCTGGACCAAGCCCCGGGCCCACCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCTGGACCAAGCCCCGGGCCCGCCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCTGGACCAAGCCCCGGGCCCACCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCGGGACCAAGCCCCGGGCCCACCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCTGGACCAAGCCCTGGGCCCGCCCCAGTGGGGAGACGGTGACCCCCAGGAGGGAGCCGGGACCAAGCCCTGGGCCCGCCCCGTGGGAGGCGCGCGTTGAGGAAGAGTGTTCCCAACAAGCTGTGTTTCCATGACGTTTGTTCAGACACCCTTGTTCTGAAAGTGTCATCACCGTCTCTAAAATTACTGAGTTATTAATAACAAGCGTGGATGGGGATGCAAAGACCTGGAGCCTCAGACCCCACTGGGGGGAATCTCACCGGGTGCGGCCCGGGTGGAGAAGCTGGCGGTGCCTTAGAAAGGCAAACAGAGTTACCTGGCAAATCTCCTCCTGGGTGTGCCCTCCTGGATGAGAGCTGAAACAGGTCCACCCAGAAACTCGTGCACGAATTTCATGGCAGAGTGCTTCACACAGCAGCCCCAGCCAGAAACAGCTCCCACAACCACCACCGATAAGGAAAGCGTGGCCTAGCCGTTGGGGGATACTGTTCACCTACGAGAGAATTAGCCTCTGACACATACTGCAACAACACGGATGAAACCTGAAAACACCGCGCCACGTGTTACCTGCTTCCGTTTGCTGAAACGCCCAGAACGGGCCGGTCCAGAGGCAGGAAGGGGGCGGCGGTTTCAGTTGCTGAGAGGGGGACAGAGGCGGGGCTGCTTGTGGGCGCAGAGTCCTCTGGGGGGATAGAGATGTTCTGAAGTCGGCGGTGGTGGGAGGATGGGGTTTCCCGTCACCTGGGTCCCCAGCTCGCGGTCTCAGGGGAGCCTTGCCACCCAGGGCTCAGCCCAGCAGGACCCGGGCTCCACAGAAAGGAAGGCAGGAAGGCCAGCGCGGCCGAGCGGCCTTCCCGACGTGGGTGCTAACGCCTGCCTCAGAGGGCCAGGCGGTGACCGCATTCTACTCCCTTCCAG
Seq C2 exon
GCAGCCGAGGAGACCCCGGGCCCCCAGGACCGCCCCCCCTCATCGAGCCAGGGATGAAAGACATCAAAGGAGAGAAGGGAGACGAAGGCCCCATGGGACTGAAAGGGTACCTGGGCCTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210:ENSBTAT00000005916:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.959 A=NA C2=0.905
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(26.5=36.7),PF0139113=Collagen=PU(77.4=98.0)
A:
NA
C2:
PF0139113=Collagen=PD(21.0=31.0),PF0139113=Collagen=PU(47.3=61.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGATGGACGGCTTTGAAGG
R:
TTTCAGGCCCAGGTACCCTTT
Band lengths:
249-1785
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development