BtaINT0041845 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:115974742-115977024:-
Coord C1 exon
chr2:115976908-115977024
Coord A exon
chr2:115974931-115976907
Coord C2 exon
chr2:115974742-115974930
Length
1977 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
ATGTTTCTTTATTCTTCTAGGCC
3' ss Score
10.04
Exon sequences
Seq C1 exon
GGTGCAAAGGAGAGCCTGGGCTGGATGGCAGGAGGGGTGAGGATGGCCTCCCAGGGTCCCCTGGGCCTCCGGGACATAAAGGTGACATGGGAGAAGCAGGCTGTCCAGGAGCACCAG
Seq A exon
GTAAAGGGTTTCCATTTCTCTTCTTTTCTCTGGCCCAGTGAATCTGAGAACTGTGTACAAGGTCCCTAGCCTCGTAAGCATTTGCCTTAGATACCAGCTCACCAGGCTTTAGGGAGACAAAGCAACAGGAACAGGAACGAATGGACCCCCGACGTTCTAATTGATACTCGACTATCATAAAAACAGGTCAAGGCCTTGTATCCATTACTCTTCCAAAGCACTATTCATTATCATAAAAGGCTCAGCCATTTCTGCTGTTCACTTTCCTATTGTGAGCCTGGCATGGCTGTACCACTGAGAGGCTGTACTGAAGATCTTAGGGTCGGCAGGGGTGGTCTCATGTCTGTAACTGGCTGAATCACTTGGTCTCTGGTTTTCTGAGTTCATTCCTCTTATCATACAGCCATCAATACATTTTGTTGTTCAGTTGCTCAGTTGTGTCCAACTCTTTGCCTACCCCATGGACTACAGCATACCAGACTTCCCTGTCCTTCACTGTCTCCTGGAATTTGCTCAAACTCATGTCCATTGAATCGATAATACCACTTAAAAAGAATACAAGGCTTTTCTTTAAAAATACTTGAGAGTGGGCCTTCGGTGAAGGCAGATAAGACCCTTTAGAATATAAATCTGAAATATAACTCATCAAGCAATATGTTAGGGCTTGAAGACTCCAAGAAACAGTTTTCTCTGTGGAGAGTATCTGGCAGTACCAGGTTAGTAATGAGAAGCAGGTGAAGGGGTGCGGGGAGCTGGGATGCTGAGGAAGGGGCCTCAGGAAAATGGGGGCTGCAGTCTGAAAGCAAAGATTGGCTTCTGTTATGTGGAAATTGTGGCCATGTAGAAGTGTGGGCCCACTGTTCCCTATACTCTGCTTTTCTAGTCTGAAATCTTAACTCATCAAATCTTGGTAAGTCAAACAAAACACATGAGCAGGCCTGATGCAGCCCACAAGCTACCAGGTTGTAGCCTCTGGTTTACAGCATAGATGAGAAAATCAGCCAGTCTTCCAGAAACAAAAACTTTTAACAAACACCTTTTTTAAAGGTGTCGAAGTCTAACTCCACCCTCTGCTTTTGGCAATTAGAAGTAGCCACTGACCTTCTTCAGTAGGTCACCCCCTTAGAGAGGCCAAAGGAGATGTCCCTGCTAATATTCTGTACAGCTGTTCATTTCCCACCAGCCAGTTAGAGATCTAGAATTTGGGCTTCTTCCACCTCCCTTTCTTATAAAAGAAAAGATACAAAGCAAAACATATGGGCCTCCCTGGTGGCTCAGCAGTAAAGAACCCTCCTGGCAATGCAGGAGACCTGGATTCAATCCCTGGGTTGGAAAGATCCCTTGGAGTAGCAAATGGCAAACCACTCCAGCATTCTTGCTTGGGAAATCCCATGGACAGAGGAGCCTGATGGGCTATACAGTCCCTAGGTTGCAAAGAGTCAGACATGACTTGGTGACTAAACAACAGACACGATGGATTCTAAACCCTTGTCCTTCTTAGAATGGAACTGACAGTATGGGAGAACCATGGAACGCGTCTAGGAGGTATAAGACAGACCAACTTTTGAGATTCACCTTTTCAGATAGCAGACTCCTGATCTAGTTGGAAAAGTCTGGGAGATCCCACACTGGCTGTCATTACCCCACCGTTCTTCTCAGCACTTATCCTTTATTAAGTATTTCATAGTTACCTTTTCATTATGCTTATTGCTTTGTCATTTCTCCTCTTCAAATAGAATGTAAGCGTAGGAGGGCAGGTATTTTCAGTTGTTTCTATGCTGATGTAACCCAAGCAGCTAGAAGCTGCTAAACCATGTCCTTGTTGAATGAGTTGTTGGGGTGCATTGCAGTTGTGTGAGGGGGACATTCCTCTCTGTTCTCTGAGTACTTAGCATAGCACCAGACAGAGGTACTCAGAAGTATCTGTTAAACGTAACTCCCTAAACCACCTTTCTTTATGTTTCTTTATTCTTCTAG
Seq C2 exon
GCCCTCCTGGGCCCATGGGGGATCCTGGGCCCATAGGGTTTGGCCCTGGATACCTCAGTGGCTTCCTCCTGGTTCTCCACAGTCAGACGGATGGAGAACCCACCTGCCCCATGGGCATGCCCAGGCTCTGGACTGGGTATAGTCTGCTATACCTGGAAGGACAGGAGAGAGCTCACAATCAAGACCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:49
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=0.266
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(32.6=37.5),PF0139113=Collagen=FE(67.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(27.6=25.0),PF0141314=C4=PU(39.8=67.2)
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:
GTGCAAAGGAGAGCCTGGG
R:
GGTCTTGATTGTGAGCTCTCTCC
Band lengths:
302-2279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]