BtaINT0038232 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008028 | CHN1
Description
Bos taurus chimerin (chimaerin) 1 (CHN1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001113247]
Coordinates
chr2:21951821-21954334:+
Coord C1 exon
chr2:21951821-21951852
Coord A exon
chr2:21951853-21954220
Coord C2 exon
chr2:21954221-21954334
Length
2368 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GAATTGACTTTGTTTCTTAGGTT
3' ss Score
7.83
Exon sequences
Seq C1 exon
GTAGAAAATAGACCAAAGTATTACGGAAGAGA
Seq A exon
GTAAGTATGGATTATCAGAAAACATTTTATAGATTGGAATATGTAAGAGAAACAGGTAAATGGATACTTTTAGTAAAAAATAAAACCAGGAGGAGAGAAGTGTTGAAGTTTGATTGAGTTAAATTATTTTTCTGACTATAAATGTAATTATAGTTGGTGAAAATATAGAACATAAAGATAAGTATTGTGAAAAATAACTGAGGAAAAATGTGCACACAATGCTAACATATAGATGCAAGCCATGTAGAGTAAATAAATAATACTAGATGTGTATGAGGGAATGTATATATTTGTATGTATGCATATATTAAACATATAGATACATATACACATATATGTAAAGATATGGGTGGTTTATTCTACATTTATACTTTTATTTTCCAATTTTCTACAAGTCATTTTCTGCCTAGAAATAACTAATGTTAAAAAGTTGAAGTATTATCTTCTGAAGATCTATTTTCTTAATGGTTTTTCCAAATTGAGTTATTATACATAGAATTTTTGTAGCCTGATTTAATATTAATAATGAGCATTTTTCTATTTTATGAAAAAAATTTAACGATTTTTAAAGTCCTTGATTCTTCTAATTATTAAAAAAAAATAGAAATATAGCCCTTTGGGGAAGAGAACAAAAATCACCTATAATCCTATCATTCCCCAAATTCATTTATCTTTCAGATAAACAGTAATGTCTAAAACAAGTATTTTTGTCTAAAGCTCTGTTTACATTTTCAGGACTCTTGTAAGTAAAACCTGGGCGCTTATGAGTTGTGGGGAGCCAGTGGTGTTCTTTACGTTATACTATAGTCATTTCTATGCTTTTGGCTGGTAGGCTGAATTTAAACTATAGTATTAAAGGTAATACTATAAGAAATATCTTAGCGCATAAAGGTTTTACTGGGAGGGAAATTTTGGGTCAACTGGTACGAATAGTTTTAAGAGTCTTTAAATACCATCATCAAGTTTTGTCCCCAAATTAGTTTCCTTGAATGAGATTTCCTTTTAAATTAATTGCGCCTTTAAAAGCAAGGAGATATTAAATTCTCTCAATTAACTGATGTCATGTAAACTTAAAATGGAGAAGGAAATGGCAGCCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACAGAGGAGCCTGCTGTCTGTGGGGTAGGCTGCTGTCTACGGGGTCGTACAGGGTCGGACACGACTGAAGCGATTTAGCAGTAGCAAACTTAAAATTTATCAATCTGATAATCTAATATATGTGTTATTACCAGGGATAGGCTACCATCTTCTTGTTCCAAAAGAATCAGAGTGGATCTGGTTCTGAACGATTGAGGAAATTTATGGAGATAAGAAATACCAGGAGCCATCATTAAACATTGTTATTCTAATTGTCATGTTGTCTAAAACATGTTCTAATTGAGCATAGTTACACGAGCTACTTTAAGACTTAAATTGAGAAAGACCAACTTGAACTCTCATAAAGTTCTTAAATTATTATTATACCATTTCAGGGCCTTTTCAATGTATCATTCCAAATTCAAGGGACTGTTGGGGTTTTTTGTACCTTTAAAAGCTATAGTCTCACTTGAGCATTTGCTTAATTCAATTTTCTTTGAGTTAATAAAAGGATATAATATATGTGTAGGTTCTTTGTAAATTGTGCATCACCATACGAATACAAGGTGATTTTATATTTTTAATACTAATGGTTAGTTACATTGATGTTTCTAAATTTTCCAGTGTTTTATGTCAGAATGTTATAGGTGAACCTACCATGTTTTATATAAGGAATGTGTTATTTGTGTTTATTCTTACTCCTTTTTTTCTGTTAATCAAAAATAGTGTTTTAGCAGGGAGTGAAAGCAAGTGTTACAGTTGTTGGCTCTTGGCTTGAGTATGCACTGATGCAGATTATGCACATTATTGGGCAATCATGCCAATTAAGGGCAACCCAGGGTCCTGGAAAATTGCCAACCATAGACTCTGAGCCAAAAGTTTGAAGCAATGCCACTGGTGTGAAGAAAGGAAGTAGGACACATTTCTGTGTATTTTTTTAGCATGTCCATATGGTCAGGCAACTACATAAGAAGGGAATTGTCCTCTTGAGAGAGGTGGTTGATCTTCCCGGAGATGGAAGTGAATTTTGTCTCCGTGATTGTTAAATGGATTGGAGAGCTACTTCGGTGCTGTTCTTGTCACTACAGAGAAGCCGGCCCAGGGCCAGGCCCTGGGAAACACAAGCACAGTTAAACCCAACTGCTCCCCTCCGATTATATGGCAGTACTTTGTCCAGAAAACTACAGGAGAAGGTGGGAGGTTTTGTTTTATCAAAAAAGGTGGAAAGCTTGCAGTTTCTGAATTGACTTTGTTTCTTAG
Seq C2 exon
GTTTCACGGCATGATCTCCCGAGAAGCTGCAGACCAGCTCTTGAGTGTAGCTGAGGGGAGCTACCTCATTCGGGAGAGCCAGCGTCAGCCAGGAACCTACACTTTGGCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008028:ENSBTAT00000010556:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.091 A=NA C2=0.038
Domain overlap (PFAM):
C1:
PF0001719=SH2=PU(0.1=0.0)
A:
NA
C2:
PF0001719=SH2=PU(53.5=97.4)
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]