BtaINT0038228 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008028 | CHN1
Description
Bos taurus chimerin (chimaerin) 1 (CHN1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001113247]
Coordinates
chr2:22078639-22081286:+
Coord C1 exon
chr2:22078639-22078744
Coord A exon
chr2:22078745-22080386
Coord C2 exon
chr2:22080387-22081286
Length
1642 bp
Sequences
Splice sites
5' ss Seq
GAGGCAAGT
5' ss Score
3.32
3' ss Seq
CCTCCCTTGTATTTTTTCAGAGT
3' ss Score
10.28
Exon sequences
Seq C1 exon
AAATTATGGATCCTGATGAGCAATTAGAAACCCTTCACGAAGCACTGAAACTGCTGCCGCCTGCTCACTGCGAAACCCTCCGGTACCTCATGGCGCATCTGAAGAG
Seq A exon
GCAAGTTTCCAACTTGGAATATACTTGTACCACATCCAGATGTTAAGAATCAAATGAAAGCAAAGGTGAAAGAGAGGTCAGGTGATCTGTTGAAGAATGAATAAATGCATAGCTATCTTGTCCCCTGGTGTGAAATCACACATTGAGAAGGCAGGCTAAAAATATTCTGTAGTATAATATGGTATGCAGACTTGATTCTTTCATAAATGGATTTGCAGTTCCAGTATATGTTTGCAGACATGTTAGAAATACCAATATTCTGCCAAGGACATGCATTAATTTTTGTGGAAAGGGAAAAGGTTGCAGCTATATAAAGACACTAGCATTAATAGAATAAAGCAAGAATGAAGCAACTTGCAAGAAAGCTCACTTTTCTTATGTCTTGCTCCAAAATAGGCACTTCAGACTTACTATTTTAGATTATTGAGTTAATGTTGCCAACACTGAAACCTGCTGTAAAAAGTGATGGAGTAAAGAAAGGGGTAAAGAGAGGAATGGAAAATAAAATATTTCAGTTACTTCTGGTTTAATGTTTTAAAGTGATGGATGGTGAGGTAGCTTTATTTCCCGGCTCGGTCACCCTCCATCTCTCCCAGTTGAAGCAAAGTTTCCAAAATTATATGACCAAATTTTAGTAGTTTTAGGGTCCCATGGACGGAGGAGCATGTTAGGCTGCAGTCCATGGGGTCGCTAAGAGTCGGACACGACTGAGCGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAGCCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCTGTGGGGTTGCACAGAGTCAGACACGACTGAAATGAGTTAGCATAGCATAGCATAGCATAGGGTTCCCAGATGTAAGACCAATCAGAAGTAAACAAAAAAACAGAACTTGACATCTACTTTGTACACCTTTAGGTCCAAGTTACCCAAAAGTGAATATGTAACTCATGGTGCTTTCAGAGACTCTACATGCTCTCCATCTTTAGAAGCACCCTAAGTTAAGACTTTTAATATGCTTATAACTTCACTTATAAATTCAAGTTTGCTGCATATGTGGATGCAGTTAAGAACTCCACACTAAAACAAAGGAGTAACTCTCAAATTATAGTCTCTGTGCCTTTGCTGTAGCAATAAAAATCATAAAAATACTTAACACTCCCTGATGAGGTTGCTTACTCCTAGCCGTTTCCTATTAATATCACTGCCACTCTCCCCCTAGATACTCAATAAACTATTCAGCTTGCAAAAACTCTCTATAGGAAACAAGATCTCACCAAAGTGGAGGGAGACCTGATGGGTCATCAAGATGACCCAGCCCCTTCCCTGCAGCTCTGGGCCGTGGCAGGAGAATCCACAAATAGAACAGAACCCACTCAGGCCAGCACATCAGCTCTGGCTTCAGCTCCAGTGGTCACCAGAAGTTTAAATTATTCCTATCATTTACTCTAAGGAGAGTCAGTACTTTGAAGTTGAGAAATAACCCAGCAGAAGGGTTGATCAGTGGACACAACCCACTTTGAATCTTGTTTTTGTTTTAGCGCTCCAGCACGACAAAGACCCCCATGCCCTACATGAAGTCACCCTCCCTTGTATTTTTTCAG
Seq C2 exon
AGTCACCCTCCATGAAAAGGAGAATCTGATGAATGCAGAGAACCTTGGGATTGTTTTCGGCCCGACACTCATGAGATCTCCAGAGCTAGACGCCATGGCTGCCCTGAACGATATACGATATCAGAGACTGGTGGTGGAGCTGCTTATCAAAAATGAAGACATTTTATTTTAAATTTTTAGTTTGAAGGAAAAAAGAAGTGTTTTACAGATGAAGGAATGTTTTATAGTAATTTAATTGGCTCTTATAGCTGAATTATTTCTTGGTTAGAAGTTTGGGCATATAACCAGATTAAAATGAAGGAACCTCCCATTGTTTTCATAGCACCGCTCAGCTGTCCTTGTAAAACAGTGAACACACGCTTTCCAGTTCTAGTAATCCTGGGTGTTTATCATGTTCAGAGAAACTCAAGCTATTGCATGATTAGCCCCCTGTTTGGCAAGGGAACCCCATACAAAGGAGACACCAAGCCTGCACCGCCCCTCATCCTGGGTCGCCTGTGGTTGTAATTCAGCATGTTTCGCAGAGTAAATCTGTCGTGACTTTGCTTTTGGGTCCTATGTCATTGATTTCTGATGCTTCTATAAACATGCACACAAATGGAGAAAACAGTACCTCTGGCTGCTGCATTGCCATAGACTATAACATATGCCTACTTTTCTCAAATGCTTCCTTTCTGGTTTCTCTTAGTTCTTCTCTAACATAGTACTTTCTTTCCAGCAAAAGCAAAATGTGTTTTCAGATTTGTTACTTTAGTAAATTATCTCTACCAATAAAAAAAGTACAACAGAGCATTTTGTTAAATTATTATTGGTCTTCAGTTGTAATTTTGTGTTTTTATCTGGCATGCATTTATTAATTTATTAAATTTGGCTTTTAGAAATAAAAAATATTGATAGCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008028:ENSBTAT00000010556:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(22.7=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(20.8=55.2)
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:
CCTCATGGCGCATCTGAAGAG
R:
CAGCTGAGCGGTGCTATGAAA
Band lengths:
356-1998
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]