BtaINT0041846 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:115972455-115974930:-
Coord C1 exon
chr2:115974742-115974930
Coord A exon
chr2:115972742-115974741
Coord C2 exon
chr2:115972455-115972741
Length
2000 bp
Sequences
Splice sites
5' ss Seq
TCGGTACGT
5' ss Score
10.06
3' ss Seq
ACGTGGTCTCCCCTGCCCAGGTC
3' ss Score
8.77
Exon sequences
Seq C1 exon
GCCCTCCTGGGCCCATGGGGGATCCTGGGCCCATAGGGTTTGGCCCTGGATACCTCAGTGGCTTCCTCCTGGTTCTCCACAGTCAGACGGATGGAGAACCCACCTGCCCCATGGGCATGCCCAGGCTCTGGACTGGGTATAGTCTGCTATACCTGGAAGGACAGGAGAGAGCTCACAATCAAGACCTCG
Seq A exon
GTACGTAGACGGGATGTGGTCACCCAGGTTCATTGCTTATGAGCAAAACTTTTGGGTTAGTTTCATGGATTCATCAACATCTTAAATGATCACTCATCTTCTATGAGATTGGTTTTTTACTTTTTCAACTACCATGCTAATTCTCAACTAATTCTATTACACCTATGACCCTGTGAGGTGCCAAGAAAGCTCATTCTAGCTATATCATTATTATATTTTTATTTCTAATTTTAAATACTAATTATTATAAAATTTAAAGTGATTAATATTATTAAATTTTTATAAAATTTTAAATTATAATTATTATAAAATAAAATTGTAAAATAATTATTTTATAATTTAGGCTATTTATAATTTTTAATAATTATTATAATCTGACTATATTATTCGTTTAAAAATAATTCTTCCTCAGTAAGTGTAACTCTGATATAAAATGCAATTTTTATTTCCCAATGTAAATGATTTAATCAGGATATGGTTGGTTCCTGGAGATGCTGCCTCAATCCCTGAGTCAATAAGATCCCCTGGAGAAGGGAATGGCAACCCACTCCAGTATTCTTTTGGAATTCATTGTCAAATGAAATACATTTGACACATAACATGATGTAAGTTTAAGGTGTACAAGGGTTGATCTGATGCATATATATATATCATAATGACTTCATTGTATCGATTGTTGGCACCTCCATCATATCACATAGTTATAATTTATTTTTTGTGGTGGGAATAATTATGATCTAATCTCTTCATAAATTTAATGATTATGCTACAATATTGTTGTCTATATTCATTCCACTAGGCACTGGATCACTAGGACTTATGTATCTACTAGTTGCAAATTTATACCCTTTAACAACTTTATTTTGAGAAAAGTAAAGCTTACTTTACTTTACTTACTCAGAACTTTACTTTGAGCATCATTCCTTAGCACTGTTTGTCAATTTCCAACAGTGGATTCGTAAGCCTCAAGAACTGACTTCTAAGTTGAGGGTGGAGTCCCTAGGTGCTGACACTTATGATCCCCTTAAGACAGCGGTGGTTGCAGTGGTGGGTGCAGGAGGGCTGTGCCCACAGGCTCAGCTGGTGGTGAGGTGTGTCCTGTCACTGGGCGTGACCCCCACTATCGGTAAGGGTGATAAAAGCATGCAGGCCTGTGGGGGGGCACCTGCTTTCTTGTGTACCACCAGGGTCACCTCCCTTGCCCTGCTCTAGCCAGAGCCACCCCACTGTGGCCGCATTCTGCAGAGCTCTTGGAATAAAATCCAAACTCCTTAATGAGATGGACAAAGCCTGCATCCTCTGGTCTGCTTTATTGGGTTGGCTGAAAATGTGTAATCCTACAGAAAAACCACAAGGAACTTGGCCAACTCAATACTCCAGCAACGCTAGAGATAGACCCAGACCTGCTCTCCCAGCCTTCCCCAGGGCTGAACTCTGAGTCCTTTGAGCTCCGTGCTCCCTAATTACCTCTGACCCTCTTTACTGCTGTATAAACAGGCCTTTCCTTTGAACCATCACCACCATCTCCAAACCTGGCCAAACCTTGTTCGGAATTCAGGTTCTGGCTTCTAATCACTTCTTGCAGCCATCCGGCTTGGATGCCTGGGAGCTCCCACTTCTCAAGGCTTGTCTTGCTGTATTCCCATGGCCCCTTGGCTCCTCCAGCTCCCCACCCCCACCAAACCGGGCTAGCAGCTTCCTGAGGATTCCTGAAGCTCTTGGAGAAGAGGTGTGCTCACGTCTCTCTCTCAAGCATCCTGGCCTGTTGCTTGACTCAGGAGAGCAATCCAGGAAAAAAAAGCAGCCTGGTCCGTGAGACCAAAGAGGCCGCCAACGTGGTCAGGTGCCCACAGAAGTAGGCTTTGGCCAGGGCCCCCCACCCCGCCACGACTCCATCCCCCACCCGCTGCCAATGCCAGACGAGTGTCTGCAGAGGGCCCAGGTAGGGAAGCTCATCCCAGAGCACAGCACTCAGCCTCCACGTGGTCTCCCCTGCCCAG
Seq C2 exon
GTCTGGCGGGCTCCTGCCTCCCCATCTTTAGCACGCTGCCCTTCGCCTACTGCAACATCCACCAGGTGTGCCACTATGCCCGGAGGAACGACAGGTCCTACTGGCTGGCGAGCACAGCGCCTCTGCCCATGACTCCGCTCTCGGAGGACGAGATCCGCCCGTACATCAGCCGCTGCGCAGTGTGCGAGGCCCCCGCCCAGGCCGTGGCGGTGCACAGCCAAGACCAGTCCATCCCCCCATGTCCGCGGGCCTGGAGGAGCCTCTGGATCGGGTACTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:50
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.266 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(27.6=25.0),PF0141314=C4=PU(39.8=67.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=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:
CCTCCTGGTTCTCCACAGTCA
R:
GATGGACTGGTCTTGGCTGTG
Band lengths:
358-2358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]