BtaINT0040968 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013369 | COL14A1
Description
collagen, type XIV, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2191]
Coordinates
chr14:84107779-84109620:+
Coord C1 exon
chr14:84107779-84107934
Coord A exon
chr14:84107935-84109528
Coord C2 exon
chr14:84109529-84109620
Length
1594 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
ACCCCACTCTCCCCCTCTAGCTC
3' ss Score
10.77
Exon sequences
Seq C1 exon
GGCCTTCTGGGGAGAGTCGACCAGGAAGCCCGGGCCCCCCTGGCTCTCCTGGACCAAGGGGCCCACCAGGTCACCTGGGGGTCCCTGGACCCCAGGGTCCGTCTGGCCAGCCTGGATACTGCGACCCTTCTTCGTGTTCTGCCTACGGCGTGGGAG
Seq A exon
GTAAGTGTCAGCCCTTCGTGGACTTTGAGCAAATCTTACTGTCTTAGTACCATAATGGTGGGGGGGACCTCTGAAAAGTAGACCTATTTTGAGCAGGAAGCAGAGCTGGAATTGCTCACTACCTTTGAAATTATCCAGAGGTCTCTTCTGTGAAGTGCAAATTAATGTAGAGGTTACCTCTTGAGGGGAAATTTAAATTAATGCCACATCTATGTCTTCCTTGCTTCCAGATGGCCTCTGACCTCATATATGATCATTGAGGGACATATCTGACAATTCTCTGGGGCCTCTCTGTGTTACTTCTGTGGTATGGCCATAATGTCCTATTAAATTTTACTCTTGTTTTGGGGACACCTCAAACTTAGAACTTTCCCCGTAATTAGGAGAGACCTGGAGATTCTGTTGGGTGACATCCTTCCCACCACATGCATTTTAAATGACCAGGGATTATTTTAAGAAGCAAAAGTGGCCGGCCACACTGTCCTTGCCTCTTATTAACTACTGGACTGAGATCCTGAAAAAATTGTGCTTCCTAAAAACATCTGTGGTCTCCATGCTAGAGGGTTGTATAACGGGACATTTTCCAACACAGTCACTCTTGGAAGTATCAAGAGAGAGGTTCAGAAATTGCTTTGGGGCAATAAACCTATTAGCCCATGAATTGAAGTTTTCTGTTTTAGAAGAAACTTAACCTTATTTCCCAGAGGGACTGATCAGAGTTTTGCTGATGTGTTTTTCTCTGTTCGTCTCTTCCCTCCCCGTTCTCTCAAACTTTCCTGTCTCTCATTAAGATCTGGTCCCTTACAATGATTACCAGCACTGACATGGAACTCTTCCACTCTGATTCCATTGGCCTGGGCAATTGGCTGCAGACACAGAACTGTCCTGCTGACCACGACCACCCAGCCCTGCCCCTGCCCACGGGCACTCCTCTCCCCTGCCCACCTGCTTCCCCACCTGCCCACCCTCTCATCTCCTGCCCTCCCTGCTCCAAACACTTAACCACGATAAGACTGGAATTTAACCAAGTCATTTGTCAGTTGTCATAAAAACCGACTGCTCCGTACCAGCCTGGGTGAGGGTGTAAGTGTGGCTGCCGAGAGTTACCCCAGACCTCCCCAGGTGGAGCCCAGGAGTAGCCACTGCCGGGTGCCTTCTCCTCGTCCCGTCTCACGCACATCGCTGGGCGTCTTTCTTCCTGACCCCCTGCTGTCCGCTCCTCCTCTGATCGCCCACCTCTGCCTCCGCCTCCTGTCCCCGGTGTTGGACTTCTAACATGAGACTGATTTTTAAAATTTATTTTTCTTTCGTCACTCTGCTGATATTCGGGTTTTCTTTTGTAAATAAAACATGTCATATTTAAGCAGTTTGGCTAACCATTTCTGCGGTGTACCTTCTTTTACTAACCATCTGAAACCTCCTGGAAAAGGTGCGCACAGCCCGGTGGATGCAGGGTGCTCTCACTTTCTACCCAAGCAGGATATCTCTGTACTTTAGAGACCAAACCTATGCCTCTGCGGATCCAAAGGAGGGGAGGACATCAATTTGTGGCTCCTGGGTTCTGTCAAGCCCCCACCCCACTCTCCCCCTCTAG
Seq C2 exon
CTCCCCATCCTGACCAGCCAGAGTTCACCCCTGTCCAGGATGAGCTGGAGGCCATGGAGCTGTGGGGCTCTGGGATCTGACAGTCTCAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013369:ENSBTAT00000017783:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.962 A=NA C2=0.962
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(75.0=79.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTGGGGAGAGTCGACCAG
R:
AGACTGTCAGATCCCAGAGCC
Band lengths:
239-1833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development