BtaINT0041823 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116033680-116034901:-
Coord C1 exon
chr2:116034795-116034901
Coord A exon
chr2:116033864-116034794
Coord C2 exon
chr2:116033680-116033863
Length
931 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
TGTGATGCAAATGTTCCTAGGGT
3' ss Score
5.19
Exon sequences
Seq C1 exon
GACACAAAGGAGAAAGAGGGCCTGATGGGCCCCCTGGACTTCCAGGGCAGCAGGGACAACACGGTCGAGATGGATATGCTGGAGAAAAGGGGGACACAGGGCCGCCT
Seq A exon
GTATGTATAATTCTCCTGCTGTAGAGTTTCACTCATACGGTCACAAAGCATCCCGGTTTAAAAAGCTAAACTCAGTAAAGCATCAACATGCTGCAAATCAGAGTCACCTTTGATTTACTGCCATAAGAAGTTGGTTGCTGTAAAGATATGGCATATTGCAGATAGTCTAAAATCCTGAGTGGTGGTTCATCACGGCAAGGCGTTCTGTCTCTAGTCTTTGTATTATTTTCACGGTGTTTATTTCCTTCTGGGACGCTTGTCTCTGTGAAGCCCCCACTGGTTTCAGGTCTGTTCAGTTGACTCTGTAGGGTGGAGGATACACACAGGTTCTGAGAATTGCCTTCAGTTCTGTTCCCTGATGGAGAAGCACTTGAGGCAAAGCAGCAAACAAGAAGGGAGGAACTAGTGCAGCTCTACTGGATAGACATATTGGCTGACGCAGGGTCCCACGAATAAATGACATTTCTGCATTTTTCAAACATGTTTTGGATGGAGATTACATGTAGCTAATGAAATTCATAAGAAAAGACTATGAGACATAATGTAGGGGATATGGTTTGATCCCTTGTCAGGGAACTAAGATCCCACATGCCTCGGGGCCAAAAAACCAAAACAGAAAACAGAAGCAATGTTGTAACAAATTCAATAAAGACGTTAAAAATGGCCCACATCAAAAAAATCTTTAAAAATAAAAGATGTAACACACATAACTTTCTGTATTTGAGGCATAACACACATGCCTGAAGAACGTATGCTGTATATGTCTGTAAAAAATCTAGGTTAAACATTTTAAATTACACGTCGTGCTATTAATTACTTCTGGAATCACTGGCTTTCTGCATGCGTTTCTGTAGCCTACGATGACAATGAGAGCTTTGTGTTCATGGCCTTTCAAAGACTGATGATTGACTTGTGATGCAAATGTTCCTAG
Seq C2 exon
GGTGATCACGAGGATGCAGCCCCAGGTGATAAAGGGCCTCCTGGACCGCCAGGGCCCCCTGGCAGAGCGGGACCTAGGGGGCCCCCAGGCCTGGGATTTCCTGGCCCTCCAGGAGACAGAGGGCAACCAGGAGCTCCAGGCTACCCAGGCAACAGGGGTCCTGATGGTCGGAAGGGTCGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:25
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(58.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.3=8.1),PF0139113=Collagen=PU(91.9=91.9)
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:
ACACAAAGGAGAAAGAGGGCC
R:
TTTCCGACCCTTCCGACCATC
Band lengths:
289-1220
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]