BtaINT0038225 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008028 | CHN1
Description
Bos taurus chimerin (chimaerin) 1 (CHN1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001113247]
Coordinates
chr2:22068310-22069285:+
Coord C1 exon
chr2:22068310-22068483
Coord A exon
chr2:22068484-22069207
Coord C2 exon
chr2:22069208-22069285
Length
724 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CCTCTGCTCTATTTTTACAGGTC
3' ss Score
11.69
Exon sequences
Seq C1 exon
ATTGTGGTTTGAATGTTCATAAGCAGTGTTCCAAGATGGTCCCAAATGACTGTAAGCCAGACTTGAAACATGTCAAGAAGGTGTACAGCTGTGACCTGACGACGCTCGTGAAAGCCCGCACCACCAAGCGGCCCATGGTGGTGGACATGTGCATCAGGGAGATCGAAGCTCGAG
Seq A exon
GTGAGGCGCTTCCAGCGGCTCAGAGCAGCCACAGCCCCCTGCACAGCCAGGCTTCCTTCTGCAGGTTAGGGGGAATGGTTCCAGATACTAATCTGGAAGTCTGAAAGCAGTTAACAAGTAATTACCAACATGATTTCAAGGTACACTTAACCAGTTATAAGAAATATGCTTAAAAATATATTTATGGATGATTCTCCCAGTCTGTAAAATTTGATATATAAATGCCAGTTTTTTTTTTCAGTTTTTATACTTTGCTTAGGTCCAAAAAGCAAAGAAATAAATGCTCTGTTTAAAACAGGCCAAACAACCAAAATCCAGAACTACGCCCTAATTAGTCTCTGCCACTTTGGAGATAATTGCTACGGGCCTATTAATATAGTTTATCTCAGTCTTCTCTTATGTAAAAGAATTTATGGTATGGCAGTGGTGGTGAAATTATTTCCCTTAAGACTTAAGGCATTTGATCTAGTTAGACAAAATGATGAGCCAAATTACAGATATTCAGGCGAGAGTACGTCAGAATTAAAGAACTGTGAGTAAAACGATTTTATTTTAGGAGAAAAGTATGAAGAGGTTTCTAAACATACATATTTCTAAACATATATGTTTCATCATTCTTCCTGACACATTGCTTCCCTAACCTTAAGTATGAGAAAAAGTTAAAATCTGAGGAAAGGACATTACCCCAAAGAGACTAATTAGCTCCTCTGCTCTATTTTTACAG
Seq C2 exon
GTCTTAATTCTGAAGGACTGTACCGAGTCTCAGGATTTAGTGACCTAATTGAAGATGTCAAGATGGCTTTTGACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008028:ENSBTAT00000010556:10
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:
PF0231811=FYVE_2=PD(39.3=74.6),PF0013017=C1_1=PD(37.7=33.9),PF0062022=RhoGAP=PU(9.1=23.7)
A:
NA
C2:
PF0062022=RhoGAP=FE(16.9=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:
GTGGTTTGAATGTTCATAAGCAGTGT
R:
CTCTGTCAAAAGCCATCTTGACA
Band lengths:
249-973
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]