BtaINT0041732 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89163178-89165255:+
Coord C1 exon
chr12:89163178-89163464
Coord A exon
chr12:89163465-89164989
Coord C2 exon
chr12:89164990-89165255
Length
1525 bp
Sequences
Splice sites
5' ss Seq
ATGGTACGT
5' ss Score
9.89
3' ss Seq
CGCCCGCTCCCCCCGCGCAGCAC
3' ss Score
8.76
Exon sequences
Seq C1 exon
GGCTGGCGGGCTCCTGCCTGGCACGGTTCAGCACCATGCCCTTCCTGTACTGCAACCCCGGGGACGTCTGCTACTATGCCAGCCGTAACGACAAGTCCTACTGGCTGTCCACCACCGCCCCGCTGCCCATGATGCCCGTGGCCGAGGAGGACATCCGGCCCTACATCAGCCGCTGCTCTGTGTGCGAGGCCCCGGCCGTCGCCATCGCAGTCCACAGCCAGGATGTCTCCATCCCCCACTGCCCGGCCGGGTGGCGCAGCTTGTGGATCGGATACTCCTTCCTCATG
Seq A exon
GTACGTGCTGTGCACCTGCTGTGACTCGGAGCACGGACCCAGGTGGAAATCGAGGTCCTCTCCCCTGCCACCTGTGGCCGTTTTTAAGACTGATCAGGGCGGTTGTTCAGGTTGGGCAGTGCGCAAAGGCACCTGGCCCTTTGTGAGAGCGGGAATGCAGCCTGCGCTTTGCTAATCCAGCCGTGTTTGGCCTGGGGCTGCCCGCATCTGGGTGGGACACAGAAGTTTGCCACCAGGCCTTTTTACAACCCTAATGAGGACGATTTGGCTATCTTGACAGCATTCCTTACAATTTGCCTGTTTACTTACCACTATCACAGAGAGAAAGTAAAGTCCAGAGGGGAGGCTGGGTCTTGTGTTGCGTTTGTATTTACTATGACTGTTGTAACTCCCATTGTATTGACAGGATACCCAACATGTTAAATGTTTCATAAACTATGTCAATCACATTATATATATATATATATATATATATATATATATAATGCAGTGTTTGCTCATCTTGTCAAAACAATAGGGGAAAAACCCTGGAATCTAGGAAAGGAAGGAAAAAGTAAACAAGAGTTGAATTTTTTTAACATTTTTAAGGGATTACTGCTGCAGTAATTTGAAGCAACAGGATCACTAGGTTCTGTGCAGGGACAGGCAACGTTCTACCTTAAGGGGCTCCTCCTGTCGGGGGACCTGGGGACAGACGGAGCAGCCCCCGTTTGCCCCTGGGTCACAGAGGAGGAAGCGCTGGACCCTCTATGTTTTAACTCCCATCGTGAAATGAAAAAGGAGCATCTTTGTCATGGAAATGCTTGCACTGTATCCTGAAGGTCAGACAGCCCTGCTCTTACGAGCATTACATCTTGAGCCACGTCAGAGGAGAAGGGAGAAGCACACTGGCGCTGGTGGTCAAGATCCACCAGCAACGCAGGAGACATAAGAGACGCCAGGTCAATCCCTGGGTTGGGAAAATCCCATGGAGAAGGAAGTGGTAACTCATTCCAGTGCTGTTGCCTGGAGAATCCCATGGAAAGAAGAGCCTGTCCACCAGTTCGCATAGGATCAGGCTTCTCCTGTCCTTCATCATCCCCCGGAGCTTACTCAAACTCATGTTCATTGAGTTGGTGATGCCATCCAACCATCTCATCCTCTGTTGTCCCCTTCTCCTCTTGCCCTCAATCTTTCCCAGCATCAGGGTCTTTTCCAATGTGTAGGCTCTTCACATCAGGTGGCCAAAGGATTGGAGCTCCAGCTTCAGCATCAGTCCTTCCAATGAATATTCAGGGTTGATCTCCTTTAGGATGGACTGGTTTGATCTCCTTGCAGTCCAAGAGGCTCTCAAGAGGCTTCTCCAGCGCCACAGTTGGAAAGCATCAATCACACATACATACACATTATTTTCCACCATGGTTTATCACAGAATATTGTACAAAGTTCCCTGTGCTGTACAGTAGGACCTTGTTTTATTTTTCCTTGGAAGAAAAAAAAAAAAGCTAACGTGTTGGCATCTCTTCCGCCCGCTCCCCCCGCGCAG
Seq C2 exon
CACACGGCCGCTGGTGACGAAGGAGGTGGCCAGTCGCTGGTGTCGCCGGGCAGCTGCCTGGAGGACTTCCGCGCCACGCCGTTCATTGAGTGCAACGGGGCCCGCGGCACGTGCCACTACTACGCGAACAAATACAGCTTCTGGCTGACCACCATCCCGGAGCAGAGCTTCCAGGGCACGCCCTCTGCCGACACACTCAAGGCCGGCCTCATCCGCACGCACATCAGCCGCTGCCAGGTGTGCATGAAGAACCTGTGAGCGCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210:ENSBTAT00000005916:44
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.2=96.5)
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:
GACGTCTGCTACTATGCCAGC
R:
TTGTTCGCGTAGTAGTGGCAC
Band lengths:
356-1881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development