BtaINT0041060 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010050 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr2:122595755-122597344:+
Coord C1 exon
chr2:122595755-122595808
Coord A exon
chr2:122595809-122597299
Coord C2 exon
chr2:122597300-122597344
Length
1491 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CTGCTCCTTTGTGCCACCAGGGC
3' ss Score
9.57
Exon sequences
Seq C1 exon
GGCATCAAGGGGGAGCGAGGCTACGCGGGTTCCCCGGGAGAGAAGGGAGAATCG
Seq A exon
GTGAGTGCCTGAGTGCTGCTCCCGCGCGGGGGCGGGAGGAAGGGCTTCAGATGGCTGGTCCCTGCCCGCCCACCTCCTCCTCCACTGCCGCTGCCTGGAGAGCTTCCCAGCTGCCCCGTGAACGCGAGACGTGACCCCAGCTTCCCAACCCCCTGAATCCTCCAGCTGCGTCTCAAGCAGTCGGTGCTGCCGGCTGGTTGCTGCGGGGGCGGCAGCTGCGAGGAGGATCCGCCGGGTTTAGTGGAGATGGCTTGGAGGGGCTGCCTGGAAGAGGGGACCTCCTCCCACCCCACGCCCACAGGCTGGAGAGCCAGCCCAACACTCTGGACCCCGCTGCCTCCAAGCCTGTCTCAGGCCACCCAGACCCAATGGTGGCTCAGCCAGTGTGCCAGACCCACCCTGAGCTCAGGTCATCAGTGGGAGCCTCCCGTGACTGGGCTCACCCCGGGTCCTGCAGCTAGTTAGTGAATTAGGGTGGACGCTGGACTTGAACCCATCCCTGTTTGTTTCTAGCCTCCCCAAACCTTTGTCTTCCCTTCCCCATCACTCATGCCGCCCACCCACAGCCGCTGGTGAGGCCAGATAGGATGCTGTAAACCCCGGTTGTGCCTTTATTCAATAGCACATCTTTCTCCAGGGGCCTTCTAGGTGCCAGGCTCTGTTCTGAAGATTCCTTGACAGATAAAACAGGCAGTTGGGCCCCTGGCCCTCAGGGAGCTAAGTTCCAGTGGGACAAGCAGATAACAGATGAATAAACAGATACACATAAATTAGGAGAGATGGGACTGGTGGAAAAAATCAAGCTGGAGCCATGAACAGGATGCTGTAGACAGAGGGTTAGGGAGGCCTCTCTAAGGGGGTGGCATTGGAGCTGAGCCTTGAATGGAGCTTCAGGGTCAAGGGTGGGGAAGGACATTTGGTTGTCCATGCTGGGGAATCCCAGAGGGAGAGGCCACGGGTGGGGGCACCCCTGGAACAGATTGGTGCCATGGATGGTTTGATAAGGTTTCAAGAGACCTGGAAAGGATAAGGGATGGCAGACCTTCTAGGTAGAGGGGACAGTCAGTGGTGTGAATGTATGGTATTCAGGGAACAGCAGTCGGACCAAACCAGGCAGAAGATAAGAAAAGGAGAGGGAAGTGAAGCAGGAATGGGTGGTTGGTATCAGATCACAGGATGCCTTGAAACTCAGCGTTCGGTTGGCAGAGGGGAGCCATGGAGGGTGTTGGAGCAAGAGGGTGTTATAATCAGAGCTGTGTTGAAGAAGAGGAGCTGGCACTTAGAGTGAACTCAGAAGTGGCAGAACTAGTTAAGAGGCTGGTTCAGTAGCTCAGGCAAGGGAAAGGGCGGCCAAACACCAGGGAGAGGAGTCCTGCAGCCTGGAAGTGCCTCCGCCACATCCCTGCCTCTGCTCTGCGCCCAGCCCCTGCCCTAAGCCCTGATCCCCCTCCCCCAGCCAGAGGGACTGATTCTGCTCCTTTGTGCCACCAG
Seq C2 exon
GGCCCACCAGGATCTGAAGGCCTCCCAGGGCCCCCAGGCCCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010050:ENSBTAT00000038016:52
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(24.3=100),PF0139113=Collagen=PU(19.0=83.3)
A:
NA
C2:
PF0139113=Collagen=PD(5.7=26.7),PF0139113=Collagen=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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]