BtaINT0041965 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106912816-106917693:-
Coord C1 exon
chr11:106917640-106917693
Coord A exon
chr11:106912861-106917639
Coord C2 exon
chr11:106912816-106912860
Length
4779 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CAGCCTTCTTTTTCCGACAGGGG
3' ss Score
8.35
Exon sequences
Seq C1 exon
GGTCCCCTGGGCAAACCCGGCCTCCCAGGAATGCCTGGTGCTGACGGACCCCCG
Seq A exon
GTGAGTACCCTGGCCCCCTCAACCTTCACATCCCCCGCCCGTGCCCACCCAGGGGTGGGGGTCGGGAACCCAGGCAGACGGCCCCTCCCCAGCTCTGGAGCTGGCTACGTGCCTGGCCCACGTTGCCTCTTCTAGCTCCTTCGATGAAGACCCCGCTGCTGGCTCAGGAATTACTGGGTTTTGGCCGTGCTTTCCATCACGGGCTGGGAGCTGCACGCGTCGGAGCATCTGCTGCCCACGCCCCCCGCACTTTCAGCTGCAACGAGGGCGGCTGGGCTCCGGGCCTCGTGTGCGTCGCCCGCGCTGCGTGTATTTTTAGCGATCACGCACTGGGAAGCAGGGTGTGCACACGCAGCTGTGGAGCTGAGCAGATGCCGCCTAGAAGCAGGGAGTGAGGGACAAACCCGCCCGCGGCCAGGCTGCGAGGGAGGGGGCGGGACAGTGACAAACGCCGGGCCTGTCCGCACCCACCAGCCTCCGCGTGCGCTGCCAATGGGCTTTTTACTTCTCGGTTATTTTTAGTGTATCTAATTGATGCCAAGTAGAGAGCCTGTTTTAGAGAATGATTAGCGAAATTAATTGTTTCAGACACAGTTATTTTGCTCTGTTAATAGTGCCATTAGAAATGAGCTGAGACGCTCAGCCCTCCACCCGTCGATTGGCGGTTGGCTGGCGTGGGGCAGGGCCTGTTTCTGTCTTCTCTCTGAAAATCCTTTGGTCCAGTGAGTCACCCATCACAGGCTTATCTGAACCAACAGATCACAGTCTCATTCCTGTTTTGAGCTGCTTCGGGTGGGTGAGGAGGCTCAGTCTCTGACGTGAGTTTGGTACAAAGAGATGAAAATTTTGCAACATGGCTTTTATGTGCTTTCACATACATCGACACCTAATTGTGTTTTCTGATGATGAAATACCTGCTTCTGGAAAATTAGGAAGAGAAGCAACATGGCGACATGATGAGCACGGCTGGCCTGCATCCTCCCGGCCGCTGCTTCCCTTTGCTGCAGCGGCGGGCGTCTGTGGGCGTTTCCCACGGTGCATTGTGTCAGAGGGCTCCCCGGGCAGCTCAGTGCCCGCCTGCCAGTGCCGCAGACATAAGAGACACGGGTTCAGTCCCTGGGCTGGGAAGATCCCCTGGAGGACGGCACGGCCACCCACTCGAGGCTTCTTGCCTGGAGAATCCCGTGGACAGAGGAGCCTGGTGGCTACATCCGTGGAGTCACAAGAGTTAGACGTGACTTAGCACGTGGCATGTTGGGAAGGAGGTGGCTGCATGGCCCCCAGTCCCCTGACCTTACCTGGAGTTCCCCTCCTGAGTTGGAACTCCAACAACTAGAGTCCCTGAGGGGTCACTCGTTTCCTGTTGGATGCTGTGGGGAAAGAGGGGCCTTTAAGGGGCACCCCGCCCAGGGAGTCAGGAGGCCAGCTCTCACAGGTCCTCATTTCTCTTCCCCCAGTCAGTGGTCACACTTGAAAATATGAGTGTACCAGGGACGCGAGGGGGGTGGTTGTGCCAGGTCAACAGTGATGACGCGAAAAGGGAAAGATCAAAAGGGGAGAATCGGAGCTGCAGGGAGAGGGACACGCAGCCCTCCAGGGGAACGTCGGAGCTGCAGGGAGAGGGACACGCAGCCCTCCAGGGGAACGTCGGCACTGCAGACAGAGGGACATGGAGCCCTCGAGGGGAACGTCGGAGCTGCAAGGAGAGGGACACGGAGCCCTCCAGGGGAACGTCGGAGCTGCAGGGAGAGGGACATGGAGCCCTCCAGGGGAACGTCCGCACTGCAGGGAGAGGGACACAGAGCCCTCCAGGGGAACGTCCGCGCCGCAGGGAGAGGGACAGAGAGCCCTCGAGGGGAACGTCCGCGCTGCAGGCTGGGGGCCACGCAGCCCTTGTCACAGGTGAATGGGGAGGAGACAAAGGGTCTGAAGCCTCTCCTTACAGAGGCGTCGCGTAGTCCCAGCCGTAAAGAGGAGACTTGTCCCTCTCCCCCTTGGTGTTGGCTTGGTGTGGGTTAAGAAGAAAGGGAAGATAGATTTCAGAGCCACTGAGAAGTGTAAGAGGTTTCAGGGCAGACGCTGCTCTGGACTCTTCGAGAAGTCATTCCAGGCACACGTGACAGGGTTCGGATAATGAATCATGGGCTCATGGAAACATTACAGAGCCAGGAACAGTCAAATTCCAGCAAGTATTCAGTGACAGGAGGAGATGCGCGATATAATACTAAATTAAAAATCGTCTTCTGACGCCAATTTTGCACGCGAACGCACAGAGCAAATAGATTAGCTGCACTGCATCACACCCCTGGCCACCGTCACCGTGCCTGGTGAGGTTATGAAGGGGTTTAATTTTCTCTTCCACTTGCCTAATTATCTACAATGAACATACATTACTTTTTTAATCAGAAAAATATCAAATACAAATAAGCTTTATTATTTTTGCATTTGTCTACAGTGAACATATATTACTTTTTAAATCAGAAAATATCAAATATACATAATTTAAGCTTTATTACTTTTCTGTTATAAAATCCTGCTGGTTACGGGATTCTGGGGAGAGATCAGCGAGTGGAAAGAGAGTGGAGACGGCCAGCCCTTCACAGCGGGAAGCTGGCCCCTCTGACTCGGATGGATTTCCTTTTGCAAACGCTCAAAATACGTGAGGGCTGTGCTCCCCCCACAAAGCCGCTCTCATCCTGGGAACACGGCTTAGAAGCCTGGCCTCCATTCCAACAGCAGTAATCACGGTGGGGACTTCCCTGGCGGTTCAGGGCTTAGGACTTAGCGCTTCCACGGCAGGAACATGGGTTCAATCTCTGGTTGGGGAACTAAGATCCTGAAAGCTGATCCTGAAAGCTGATCCTGAAAGCTGTTTGGTATACCCCCAAAAAACCCAGTACCCCCTAAAACACAGTTGGTCGTGGCAATGATCCGTCCTTCTACACTATCTGTTCCAAAACACTGTGACCAGGTCTATTCTCTTGTTTTTAATTTTTTTTTTTTTACTGTATCAGGTCAGTTGTGACACGCAGGTTTTGTTGCCCCAAGACATGTGGGATCTTAGTTCCCTGACCAGGTGTTGAACCTGAGTCCCCTGAATTGCAAGGCAGATTCTTAACCCCCAGAGCACTCGGCAAGTCCTCAGGTCTGTCCTTAGGGCCACCGTGTAAGTAAGGTCATCGCCAGGTGGAGGGTCGGCTCGCTCCCCAGATGTGGGGCCCGTGCTCGTTTGTGTCCGGGGCCTGCCGTCACCACCCACAGCTGCCCGTGACCTCAGTCCCTTCACGGAGAAGTTCCAGGTTTGGTGGAAACGGTACAAGAGGCCCAGGAAGAGCCCACGTGGCAGGGGAGGAGGCCTCCCCTTTCCCCAGCGACCCCGGGGCAGGACGTGTCCCGGGCACACTTAGGTGCAGCCCTGCCGGCCCGGGCGCAGGCGGTGAGCCTCGTCTCAGGAAGGTGGAGGGCGGCCGTGTGTCCCCTCCAGGCCCGGGCGCAGGCGGTGAGCCTCGTCTCAGGAAGGTGGAGGGCGGCCACGTGTCCCCTCCAGGCCCGGGCGCAGGCGGTGAGCCTCGTCTCAGGAAGGTGGAGGGTGGCCGCGTGTCCCCTCCAGGCCCGGGCGCAGGCGGTGAGCCTCGTCTCAGGAAGGTGGAGGGCGGGCCGCGTGTCCCCTCCAGGCCCGGGCGCAGGCGTGGTCCGGCCAGCGCCTGATTGTCCTCACAGGCTCCCAGGCACCACACCCCCTCCAGCAAAGGAACTTCCGCATTCTCCCCCTCCCGTGGCCACCGCCTCAGGCTGTCCGCAGTGGCATCAAATCCGGTTCACAATGATCGCAAATTAAAAAGAACACACACAAATCATGTGTTCAAGTGGGTGAGGTCCGCGTCCCTGCAACGCTGCTGTCCCACAGGTAGAGCTCAGAACTTTGGAAGGATCGAGCTGAGAGCAGTCAACCCCCTCTCTCGTTATACACCCTCGAGAGAGGACGCCCAGAGTGGGCAAGCGACTCACCTAAGGTCACACAGCAGCCCGGGGGTTCCCAGGATTAGAGTCAGGCTGCCCTGGCCTGCCAGCATCCTCACCCCACACCGTGGCTTCTCTTTACTGGCGCCCTTGGGGGCAGGACCCCGTTTCTTGACAGTGAACACTCAGGTTCTGTTTTTATCGTCCGTGTTTGGCTCCTGAGCTCAGAGGCACTGAACTTAGTGACCAGCTTGGGTCTGAAAGTCAGAGAAGGTGAAGTTCCTGAGAATGGCTTGATGGCACCCGGGTAGAGAGGGCCCTGAGCGGTTCCTGGGGCCCCCGCTCTGCATCTCTGGGTGGATTCTCCCCTTGCCCCCAGCTTCCCTCCCCATCTGTGTCGCCTGGGGTGACGACTGAAGGCCTGGGGTGCCTGGGAACCTGGGAGGTCTGGTCCCCCTTCTCTGTCCTTGCTTGGCCACTAGTGTGGTTTTGCTGGTTGACCTTGAACACATGGCCTTGCTGTCACTGACCCTGCCCACCGCAGGCAGGGCGCGGGCTGCGTTGGGGCCCCGGCGCACCGTTGGGCTGGGGCCCGTCTGTGGGTTTGGAAGCTCGTCCCCTGCCGTTGCCGCACCCCGGCACCATTCCCATGTTAACAGACGAAGCCACCGAGGGTCAGGGCCAAAGGGCGGGGGGACCAAGGCGCTGCGGGGAAGAACAGGAGGGACCCAGGTTCTGACCCTCACACTGGAGACCGCTGTGGGAGAAGCCTGCGTTCCCAGCGGCCACTGACTAACACCAGCCTTCTTTTTCCGACAG
Seq C2 exon
GGGCACCCTGGCAAAGAAGGCCCTCCAGGAGAGAAGGGAGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:31
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(11.6=53.3)
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:
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