BtaINT0060642 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008140 | FAP
Description
Bos taurus fibroblast activation protein, alpha (FAP), mRNA. [Source:RefSeq mRNA;Acc:NM_001098001]
Coordinates
chr2:34329737-34331772:+
Coord C1 exon
chr2:34329737-34329840
Coord A exon
chr2:34329841-34331636
Coord C2 exon
chr2:34331637-34331772
Length
1796 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAT
5' ss Score
7.84
3' ss Seq
CTGTTTTGATTTGTTTGCAGTGA
3' ss Score
7.59
Exon sequences
Seq C1 exon
GCTGGAGCTAAGAATCCTGTTGTTCGGATCTTTATCATTGATGCCACTTACCCTGAGCATATAGGTCCCAGAGAAGTGCCAGTACCAGCAATGATAGCCTCAAG
Seq A exon
GTATATTTATCTCTGATGCTCCCCACCTTTTAAACTGAATTTTAGCACTGAAATTTCTTCATCAGGGTTTACATTTCTTTTCTAGCAAGTTTGCAATGACTATTGTACAACAAAAATAAATAAATAAATTAGCATGCCAAGCTAAACACATAGCAAAATTAAAATTCACAAATAAGTTTTCTAAACTGATGTGAACATACTAACCCTTGACATACATATAAAGATGACCAGAGTACTCAGTCTAAGTGCTGCTTCCCTTGGATATGTGAGTGTAAGCTAGGGACAAACAAGGAGATAGTAAAATTTATGCATGCTCTCAGCTTGGCTTCCTTCAAGTCTGGCCTACTTTTTCCCAGTGTTTGTGGATCATGCTTATTATATGTGCACCTCAAACAGGAGAAGATAAGCCAACCCCCTCCAAATATTAGTGTTTTTCACTAGGATGCAGTCTATTTGAAGTGTCCTGGTTGTAGCATTATCTGTTTGTGGATGAACTGCAGGCAGACCTGGACAGAAGCATTTTCATTTCTGTGAAAGGTACCAGCATGGTACCCATTGAGATCTTGTCTAATTGATCCTGGTCATTCTGGTTGACATGGAAAACGGGGAGGGGTCCATAAGCCCTGTCTGGCTGGCATCCTTACTCCTTCCTATATTCTCTCAGAACAAGGCTTGACTCCTCTTCTCCTGCCTCAGCAGGTAGGTCAGCCAGGGCCAGATGATTGATTAATAGGAAAAAAACACCTCATCAGAGGCCTCTGCCGGATTTTGCCAAGGTGAATCCACTCTCGGATAATCATTCTTTTTTTTTTTTTTCAATTATCCATTATTCCCCACCCTAATCTGGTTGATGAAAACTGGACTAAATATATCTGATTTTTTTATGCATCATTCTCCTCCAGAGGCAAGTGGAACAAAAGAAAGCATCATTTGTGCATCCGTAATATACTAACTATGTAATAATATCTAACATTTTTTGAGCACTCACTATGTTGTATGTATAGTTTGTAAGCACTTTAAGCATTCTTAGTAAATCTTTACAGCAACCTTTCATACTGGTAATGTTATTATTCCCATATTATATAGAAACAGAGGCACAGATATGTTAGTCAAGGTAGTATAACTAGTAGGAGATAAAGCCAGACTCTGAACCAGAGATCCCTTGTAGCTCTGTGATTCCTTTTACAACAAGGTCCAACATTTTGTGGTTTATTTACATTGTTGTTACATTCACCCTCAGAGCCAAGTAATCATTGCTTCCTTTCACCAACATCCACTTTGTGCCAAGCACTGTTTGAGTTACTTCGCATACACTATCTCTGATTATTATACTAACCCAAATTTCAACCCCTGACCTGTAGCTAAAACAGCTTCCAACACAAACCTGCCTGGAAATAAAGGTGGTCTTTTATCCACTTAGCTCTCTGTTAATTAGTTAAAAAGTGAAAACTTGAGTTCAGCTATGGAAAAATAGGCAATTTAATGCTTTTGTCCTATAAGTTGGCCAATAACTTTGGCCTTGTGTATTAATTTTTTTCCTAAGATATTAAAATCCCAACTGGGGAGAAAATTCAATTATAAAATCATTCTATTAGATCAGTGAACTCTTATATGTTCTCTAAAACTTAGCAGGTGTATTTAAATTTTTAATGTTTAAAAGAATATTTTGCCTTCCTTACCTGTGGCTTAAGTGTTTCAGAATAATAAAATATGTCCTTTAGAAAACACAAATTAAGAAATTATTTGAATGTGATATTGATTTATAGTTGTGACTTTCTGTTTTGATTTGTTTGCAG
Seq C2 exon
TGATTATTATTTCAGTTGGCTCACATGGGTTACTGATGATCGAATATGTTTGCAGTGGCTAAAAAGAATCCAAAATGTTTCAGTGTTGTCTACATGTGATTTCAGGGAAGACTGGCAGACATGGAACTGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008140:ENSBTAT00000010702:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0093016=DPPIV_N=FE(9.2=100)
A:
NA
C2:
PF0093016=DPPIV_N=FE(12.2=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:
GCTGGAGCTAAGAATCCTGTTGT
R:
GGACAGTTCCATGTCTGCCAG
Band lengths:
236-2032
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]