BtaINT0042008 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106862054-106865971:-
Coord C1 exon
chr11:106865903-106865971
Coord A exon
chr11:106862288-106865902
Coord C2 exon
chr11:106862054-106862287
Length
3615 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CCCGTCCTGTCGCCCTGCAGCTC
3' ss Score
11.89
Exon sequences
Seq C1 exon
GCCAGAATCACTTCTTGGCCCAAAGAAAACCCGGGTTCCTGGTTCAGTGAATTCAAGCGTGGCAAACTG
Seq A exon
GTAAGACGGCCTCTGCCGAGCGTGCGGTGTGGTTTAAACCCGCCCGTTTCGTATCTTGCAGAGTAAAATGGCCCGCTGGCCCAAAGAGCAGCCCTCCACCTGGTACAGTCAGTACAAGCGAGGGTCGCTGGTAAGTGGCCCCGGGGCTGCCTGCTTGCGGCTCGGCCGGGCGCGGCTGTGCATGGGACGGACCCCCAGCGCCTCACCTGCTCTCGCCCTTTGGCCAAACTGCTCCGCCTCCATGACCGCCAGGCTCAGGCTGGCCCCTCCTGCCGCGCCGACGGGGGTCCACTCTAGCCGAGGGCAGCTGGACAGCTGTCTGATCAGGTGGAGGGCGTGAGGCTGGCTTTCAGAGCCCCCGGCTGGGTCTGCCAGGAACCGAGACCACAGACCCCAGGAGTGGAGGGTGTATTTAGCTCAGTCCTAGCGGGCAGCTCGGATGGAGTGAGCCCCGGCCTGTTAGGCCGTGCAGCCCCTCCAGGGCTCATGTCCCGGGCCCGCCCTTGCTGCGGCCGGGGCCGAGGGGCCGCGGGCTCCTCCGCTGTGTCCCACACAGTCGTGCTGGTCCCTGTGCTGACTTCTGGGGACCCAGTCTTAAGCGGTCTATCTGGAGGTGCAGGCAGCTGGCGTCCCTCGAAAGGACTGGACTTCGTGGGTCTCCAGGGGTCGAGAGACTGGGGCCCGTTGCGCCCGATCCCCTGGGGCTGTGGTTGCTTCCGCCCGGGAGGGCGTTTTCCCCTCCAGAATGTTCTGGGCCTTTGACTCGGGCCCATTTCTGGAGCCCAGCACAGAGTTCTGTGCCCCTTCCCGATGAGCTCAAGGCCCAGGTTCCAGACGCGGCCACACTGCAGGTGCCACCAGAGCCCCTCGCTTCCTGCGTCCCCTCCTCCGCCAGGGTCCGCCTGGCCGCCCTGGAAGGACATACTTGTCTCTCAGAAGCAGCTCTCGGGTCCAGGGTGTGGGCCTGACCTGACCCTCCGTCCTCAGTTGGCTCCCCAGGGGCCCAGGGCCGCTCTCCCCCGGGACTCAGAGCAGGGCCTTCCACCAGTCCACCCTGGGGACCCTGATCCAGACCCCGAGGTGCTACGTGCTCACTGTTAACAGCTCACGCCCCGTGTCCTTGAGCCCCGGTCACCGAAGCTCTTTCTAGACACAAAGTTTGCACTCGCCTTGCCTTGTCGTGGGCTTCCTCTGTCTCTGGGCAGACACCCAGGCACCCTCTCCCCCTCCTTCCTGCTGGCTCTCCTCCCCGTGCCGCCTTGGGGCTGTCCTCAGGACAGAGCCTCTGGCATGCAGAAGGACCTGAAGTGGGTACCCCTTGGGAAGGCAGTGCCCAGGGCACTTGAGCCCGGCGGATGCTGGTAGGTGGGCGCAGGACTGAGGAGGAGGGGCCGGGGCCCCTTCTGCAGCCGTGCTGCTGGGCTTCTCCAGCCAGGGGCCCTCAGCCCCATGCCCACCGCCTGATTCCGTAGACGAGGGCGCAGAGCACTCGCTCTCAGCCGCCGGCCCGAGCCCACCTCCTCCTTACGTCCTGCTTCGCGGACAGTTGACCAAGGCCGGAGGTGAGGGACGGTTCCGGGGATGGCCACGCGTCTCCTCCACGTTCCAGCCGCATCGTTTCTAGCTGCCTGTGACCATCACAGTGGGCATCACAGGGCATAGACGCGGTTCCCCCGCAAAGAAACAGGCGCTTTTCCCAGCCGGCTGCCCTGGGCGTCACCAACGGGACGCTGCACGGCCCCTTTCCCCAGGAGGGGAGGGCTCACCCAGGGCTCTGAGATGCCAGCGTAGGGCTCGGGGTGGGCAGAGCCCGGGCCTCACCTCTGCCCGGCTCCGGAGCTTCAGGTCCTTCTGTGTGCAGCACTGCCCCCGCCTCTGTGCGCATGCCTCCTGCCTCCAGTCAGTCACCTTCCCTCCAGGAGGAACGCCGACAGCCCAGACCGCGGTTGGTATCCCCTCTCTCTCCTCAAGGTCCAGCTGGAGGTCGGTGGCCGGCGGCCACGTGGGGAGCTGGCTGGCCGCTCTGCGCTCTCCCCGCCCTGGTGGGGAGGAGCAGGAGGCCGGGCCTGGCTCGCCGCCATCAGCCATCCTCACACAGAGATCTCTAAATACAAGGACAGTAGTGACTTCAAGTGCCCCTCGTGTGATCAGCACGGGTGTTTGGGGCCCTTCCCGTGGATTTCCACGTAGAGTAGACCGTCTGTAATCCTTTCTGGCTCTTCTTGGTTCCTGAGGATTTACACTCGGCTCTAACCCTCTTATTGAACAGAATGGCCAGGGCGTGTGTCAGAGCTGGTCACAGGCGTCCCCGACCGGGGGCAGGCATCCCGGGCACCAAGCTGCCTCTGTGTGCTTGGGGGCAGCCAGTGCGCTTGCCTGGCTGAGCCAGGCGCCGGGGTCTGAGCCAGAGCAGCGGTGGAGCACCTGTGTGTCAGGAGGACCTGGGGTGTCAGGCCCTGATGTTAGCCCGCCCCTGTCGGATGGGGACCCAGCACGGGCCGAGCTCGCTCTGCTGGGTCCGAGAGGAGGGCCTTTAGGGGAGGAGAGACCTGCCTCATCCCAGGGATTTGGGAACCCCCACCCCTGCCGGGCACAGCAGCTCACAGAGCCGCTATCGAGAAGGTGCAGAAGCTGATCTGTCCCTCAGGGCACCCGGCACCGGCCCACTGAGCTCCCAGCCCGTGACGCCAAGGAGTCACTTGGGAACCAGCCTGCCCTCTCTCCTGGGTGTCTCGCCCCGACTTCAGGCTGCCCGCTCACGTGGGCAAGGCTGACCCCTTGACCCCTAGGCCTCCACACTGGCTGTGCTCTCCCCTGGGTCCACGCCCGGGGAGGGGTCAGCAGAGGCCTTCCCCCTGTGCTCAGAGAAGTGCCCAGTCCCTCCAGGCCTCTGGCTCTTGGCCATATGGCCCGTGACCCTCTCACAGGCTGGCCCTCCCGTCTGCTGGCCAAGCACCACATATCTCACGCCCAACCGGCCCATCCCTCTCCAAGGCCTCCTGCCCTTTCTGTGTCCAGTTCTCACGGCCCCGGTCAGGTCTTTGTACATCATGGCGACCAGCCAGTGGTCAGCATCATCTAGTGAGCACCTTCCTTATGCTGCCTCAGGGCACAGAGACAGGATGTGCACGCCAAGCTCCTGTGCTCCGGGCACTCTCGGTCCAAGGAGGGCCAGAGACCAGGCCCCAGGGACCCCAACACAGCAGTCCAGTGCTGGTACGGAGGGCCCTACAGCCATTAGGAGAGACGGACACTGAGCCAGGCCACGCTGGGCGAGGACATCTAACCCAGGCAGGCTTCCTGGAAGAGGAAGCATATGAGTCAGGCCCCGGAGGCTGAGTAGGGACCAGCCAGGCAAGGAGTGGGTGGGTTACTTGGGTCCTTGAAGGAAACGAGGTGGGGTTCACTGTGTTCCAGGGAACCCCCCAGAGAGCCAGTGAGTGCTGGCCTGGGGGCCCAGGTGTGTGGCTCCTTTCCAGGTGGGGCCCTTGGCATGGCCCACACTCCAGAGGAGACAGCTCAGGGCTGAAGCTCCCAAGCCTGCCCATGTGGACGAGGGGCCTTGGGCGGCCACGTGTTCCCACCCCGCTGAGCCCCCGTCCTGTCGCCCTGCAG
Seq C2 exon
CTCTCCTATGTGGACGCCGAGGGCAACCCCGTGGGCGTCGTCCAGATGACCTTCCTGCGGCTGCTCAGCGCCTCCGCCCACCAGAACATCACCTACAACTGCTACCAGTCGGTGGCCTGGCAGGACGCCGCCACGGGCAGCTATGACAAGGCCATGCGCTTCCTGGGCTCCAACGACGAGGAGATGTCATATGACAACAGCCCCTACATCCGCGCCCTGGTGGACGGCTGCGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:71
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.130 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141013=COLFI=FE(10.4=100)
A:
NA
C2:
PF0141013=COLFI=FE(36.3=100)
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