BtaINT0041978 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106894565-106897489:-
Coord C1 exon
chr11:106897436-106897489
Coord A exon
chr11:106894619-106897435
Coord C2 exon
chr11:106894565-106894618
Length
2817 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
GGCTGACTCTCTCTTCGCAGGGT
3' ss Score
9.56
Exon sequences
Seq C1 exon
GGGCCCCCAGGCAAGGACGGGCTCCCGGGGCACCCTGGACAGCGAGGCGAGACG
Seq A exon
GTGAGTGTGGGCAGCGCCGGGGGATGTGGGCGCCGCGCCCGACCTTCACTGCCGGTCGGCTCAGGCAAGGCTGAGGCTCAGCCTTGGGAAGCCCCCCGAGGGCCGGCCGGCTCCTGTGGCCGCGGGATGCGCCCTCTCTGGAGGGAGCTCCACAGCCTCCGAGCAGCCCCTTGGCCTCTGTGTGTGAGGGCAGGTGTCGGCTTCAAGCCGTCCTGGGCAGCCTGGCCCAAGGTCACACGTGCAACCATCGTGACGCCAACGGAACCTAGAGGAGTGGCCCCTGCCTTCCCCGGGAGGGTCGGAGCGCGGCCCAGCGCACGCCACGTGCGTCTGAACTGGACACTCCTTGGGCAGGTCCTCCCTTTCCAGCTTTCCGGTTACTTTATGCCACCCCCAGCCCTGTCTGTCCCGGCCCTTGCCTCGGGGGGGATGGCAGGGAGGCAGACGGCTTCCCCCAAGTGCCCTTTTCAGTAAGGGGGCAGGCGGCCGGTCGGGCTGGAGTTTGGGCCCTTGGCTGTGCTCAGGGCCAGCGTCTGCTGTCAGGGCTCACCTTGGCCTTGCCCTGACCTGTAGCAGCGCCCGCCACAGTCTTTGACAGCTGGACTTAATGGACGCCCACGTTTTTTAGTTCTAGAAAAAGCACTGGGGTCACTTCCTGGTCCCAGGAGCCACGGGGGATTCAAGCGAGCTTCATGCTGAGTCCCCCCAGGCCTGTCCCTGGGAAGGGCGTGGGCACCCTGTGACCTGGGGGCTCCCGCTCTGGACAGCTGGGGTTCGCAGCGCCTGGTGACCTTCTGGCCACCATAGTGGTGGGGACTGGCCCACGGGAAGGCCCCCTTGTGTCTGCGTCCGGCGTCCATGTGGTCAGAGACCTCTGACTCTCCCAGGAGGAGCCGGCCCCTTGAGAAGTGTGATCCTTAACAGCACACTTAATACGTCTTGGTGCTTCTTAAAAACATCCCTGGGTCCCTTTTTGGCTCGTGGTGATGAAGAGTCCCCTACATGTGCCGTCCTGGTGCTCCGTGGCAGAAAACAGAGTTCGCTTTGCTCTTTTGTTTCTGGAGAAAAACTAAAGCACCCCCAGCTTTGCACGCTTTTCTCCAGTGCTCTCCTGAGCAGATCGGATGGAAGGCTTCTCGTCTCACGGTGCGCACTCTCCCCTCTGCCTTGTTCTGGGGAGAGGCTGGCAGAGTGATTAAGCCGCTTGTTTTGCTGGCAAAGCAGGGCAGGTTCTTCCTGCCCCCCCACCAGGCCTGGCTGCCCCGGAGATTCAGGGGCACCCCCATCTGGGCCCGCCTGGGGTGTGGCGTCCTCCAGGGGTCAGTCCAGATGCCCTGCAGAGAGGCCCTCCTCGGGGTCATGACCTGTGCTTTCGTTAGAGAACTGGAAACACAAGAGGTCGTAGCACCTCCTACATGCGAGCCCAGAGCCCGCTCGTCACAAGCACTGAGATGGACCCCGGCCTCAGCTGGCGTGGGTGTCCCCCGGCGGACCACACGCAGGCCTTCCTTGCCTCCACGTGGGCACTGCTGCCCAGCCCCCCGAGCAGGGGAGATGCCTTCGATCTGTCCAGCATGCCTTGTTTCTGACCCTGTAAAGGCTGCTGGCCTTGCGGCTAAGATTAAGTGTAGTATGGGGGCTTCACAGCTGGTCGGTGGTAAAGAATCTGCCTGCTGAGGCGGAGACACAAGAAATACAGGTCCGATCCCTGAGTTGGGAAGATCCCCCGGAGTAGGAGATGGCTGCCCACTCCAGTACTCTTTCTGGAAAACTCCATGGACAGAGGAGACTGGTGGGCTACAGTCCCGGGGGCCACCAAGGGTCGGACACGACTGAGCGCACAGAGGTCTCCTGTGGGGAGTGCGGCCTCGGCCATGGCCGTGCCAGTCCCGTGCGTGCAGCTCGGCTGGAGCCCTCCCAGACTCTGCTGTGAAGCTGCCTCTGCTCTGGGTCTGCACAGTCCAGCGGCTGAGCATCAAGTGTCCCTCAGCTGCACACTCGCTGGCTGTCGTGCTCTGGGTCAGAGGTCCTTGCCCTTCAGCCCCGTGGGCAGCTGGCCCCGCGGCTCTTGCTGCGGCCTTAAACGAGCCGTTTCCCTCTGCGGACGCTGTAGAGTTTCCACTGAAAGCCTCCCGGGCGTAGCATCTGCACGTCTCCCCCGGCGTCACGTGGCGCCTGCAGATGGCATCTTGTCCGCACGTGCCGAGCTCCGTGGAAATGAATGCCGGAAATGAAACCCGTGCTGCTCTGCCGTCAGCTTCGCCTCTGGGGGAGAGCGTGTGCAGAGCAGCCAGGCGGCCGGGTCCGTGCCAGCGAGCGGAGCAGAAACAAGCGGTTCCTGTTGAGTCGAGCTAAGAATACCTCCCAGCTGCCACACTGTGGAAGTGGCAGGTCCCCTCTGCGTCCGGATTTCAGTGGGTGCCGTATAAAACCGGCTGTCCTGCCCCAGGGGCCTTGGGGACACCAGCAGGACAGTTCCCGCACAGTCACTGACGAGAGGCAGCCCAGAGGTGGCTCCCGGGTGTAGTTTCCAGCAGCTGTGACACCAAGTCTGCTCAGAAAACAGACACTTAGTGACGTGAGGAGGACGAACGGTTACAGAGTATATTTCTCAGAGCAAGACGGGGTGATGGAAGCAGCTAGTGAAACGATCCTGTCTGGTTTCCTGACCTTCCTAAATTCATGCGAAGTGGGACAAGAGAAATGGCCCTTTTCAATGAGGTCTCGGACGTCAACTGTTTTGGGGTGGGGTGGGGGCTGGGGTGACCTTCTGTCTGCCGCTTCAGCCGTCTCAGCGGGCTGACTCTCTCTTCGCAG
Seq C2 exon
GGTTTCCAAGGCAAGACCGGCCCTCCAGGCCCCCCAGGTGTGGTCGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:44
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(23.6=100)
A:
NA
C2:
PF0139113=Collagen=PD(19.4=77.8),PF0139113=Collagen=PU(24.3=94.4)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development