BtaINT0040902 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011741 | COL13A1
Description
Bos taurus collagen, type XIII, alpha 1 (COL13A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105433]
Coordinates
chr28:26363682-26365255:+
Coord C1 exon
chr28:26363682-26363726
Coord A exon
chr28:26363727-26365228
Coord C2 exon
chr28:26365229-26365255
Length
1502 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
TCTTCTTTTCTCTCACACAGGGT
3' ss Score
11.21
Exon sequences
Seq C1 exon
GGAGAACGGGGAATGCCAGGGATGCCGGGCAAACATGGAACAAAG
Seq A exon
GTATGCAGCTCCCCCCACTCCCCAGCAGCTCCCCAGCCGCAGTGCCCTCCCCTACCGCCTCCTCCTCCTGCATCCTGTCCTCCCATAAAAACAGAGATGGGGTGCACATTTCTTCTCATCCTCTCCCCTTGCTGCCTGGCCTGTTGTTCAGGCAGGGGTGTTCCTTTTCAGCCCATGAACCATCACTCACCAGCAGCCTCCCAGCCTGCCCAGGCCTCCTCCTGGGCATCAGTGGGTCATAAAAAGAACTTCTCAGGTACCCTCAGCTCTGGCTGCAGTCCTGAGACCCATGTGGGAATCAGGATCTCCTAAAAATGACATTCGCTTGAAATTTACTAAGTGCTGTGCTTGGCAGCTTATTTACCTCAAAGTTGGTGGTCTGGAGTTGGTAAGGAAGTAGGGTTCACTCCCAGCTGCTCCCCAGTCCACTGGGACTTAGAACTAGAGGGCTCCCTTAGGGAGAGTCCCACAGGCAGCCTCAGAGGCCAGTGAGCTTAGTAAACTCAGCCACCTGCTGCTGTTCACTTCCCCATGGCTCTTCTTCCCCCCCTTTCTCCTCCATCTCCTCCTCCTTTCGTATTCCACCCGTTCCACCCAGGGACGCCCCTCATCTAGCCCAGCCAGGGGCTGCCTGCCATGGTGCCCTTTGAGTCTCCCAGGAGGGTCTAGAAGCCCAGGGAGCCTGGCTGAGCATAGAGGGTCTTTCTCAGGCCACTCTGTCTGAGCCAAGCTCAGCAACCCCCTTCCCGGTGTACCTGGGCGGCAGCCCAACGTCTCCACGTCTCATGTCTGGCCACTTCTTCTGTGCACCGCCCCCCCTCCCCCTGCCAGGTGAGAACGTCCCCATGCCTTTCCTTGTCTTGCCAGGGGGCTCCTGGAACCACTGTGGCCAGGATGAAGGTCAATGGACCTTGTAACTCAAGACCTGAGGGGCATGATGGGAGGGGTGGAGAGAGGACAGAGTTGGGGTTTCAGGGGCTCAGTGGGTGGCCATTGGACCAAGGCAGGAGCAGACAGAATTCAGAACCGTTGCCCTTGAAGCAATATGTATGCCAGATGCTCAGCTTGAACAACAGATGTTTAAGTAAGCCACGCAAGTGACTGGCAAAGGTTTACCATTCTCAGCTGAAGGTCCCACCAGCCTGCCAATGTGAAAGGAGTCTAGTGCTTTGCTTTACTCTCCAGAATTCAGCCAGTGGGCAGGAACACTCCCGAAGCAGAAATAATGTGGATCTCCTCCAGGACATTTACAGGGATACGGCATCCAAAGCAAATGCCCCTTCCTTCCTCTCCCTCCTCCTGGGCTGCCTGCCTCTCACCTGCCATCGTCTCACCTCGGGGAAGAATAAGGAACAGTCCAGGAGGGGCCCAAGTCCGAGGCAGAGGAAAGCCCTGAGCTGACCAGACACTTCTGCCCCCAAATGGCTTCACTTCTCTGCTCCTGGCCTCACTCATCTGGCTCTCTCACATTCTTTACCAGAGTCTTCTTTTCTCTCACACAG
Seq C2 exon
GGTGAACCTGGGATCCCAGGAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011741:ENSBTAT00000039811:16
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(19.7=100),PF0139113=Collagen=PU(3.1=13.3)
A:
NA
C2:
PF0139113=Collagen=FE(11.3=100),PF0139113=Collagen=FE(12.3=100)
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:
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]