RnoINT0169015 @ rn6
Intron Retention
Gene
ENSRNOG00000001335 | Zkscan1
Description
zinc finger with KRAB and SCAN domains 1 [Source:RGD Symbol;Acc:1560616]
Coordinates
chr12:19238150-19239204:+
Coord C1 exon
chr12:19238150-19238649
Coord A exon
chr12:19238650-19239053
Coord C2 exon
chr12:19239054-19239204
Length
404 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTATCCATTTCCCCCCTCAGGTC
3' ss Score
11.46
Exon sequences
Seq C1 exon
GAACAGTGCAGAAACCAATAGAAGATAGTTGCTAGGACAGAAACTGCAGCCTGACCCTGTTGGACTCCACCTAAATGATGACTGCTGAGTCAAGGGAAGCCACGGGTCTATCCCCACAGGCTGCACAGGAGAAAGATGGTATAGTCATTGTGAAGGTAGAAGAAGAAGACGAGGAAGACCACATGTGGGGGCAGGACGCTAGCCTTCAGGAGACGCCACCACCCGACCCAGAGGTGTTCCGCCAACGGTTCAGGCGCTTCTGTTACCAGAACACTTTTGGGCCTCGAGAAGCTCTAAATCGACTAAAGGAACTTTGTCATCAGTGGCTTCGACCAGAAGTCAACACCAAGGAACAGATCTTGGAGCTGTTGGTACTGGAGCAGTTCCTGTCCATCCTGCCCAAAGAGCTGCAAGTGTGGCTGCAGGAGTACCGGCCTGACAGTGGAGAAGAGGCCGTGACTCTTCTGGAAGACTTGGAACTTGATCTGTCAGGACAGCAG
Seq A exon
GTGAGAAAAGGGATAGCACCGGTATGTGTAAGAAGACTTAGGGGTAGGCTCAGAGGGGAGTGTTTGGAGCAGTTGACCTTGCCTATTGCTCTCCTGGACTCTCAAAGACTTCTGGGAGCTTGGCAGTGTGACTCACTCCATTCTAGAGCATGTGTGTAGATAGCATCTGTGAGGCTCAGGGTTCAGTGGCCGACCATAGGAAGGATGAAGGGGTGGGGGCTCCTCTTTTCAGCATCCACTGGATACTTAGAGGCTTTTCTTTAATTCTTCTAATTTCTGTTTTAAAAGTGATTTGCTAGGCCAGACATAGTGCTTCATACCTTTAATGCTAGCACTTGAGATGCTAGAGCAGGAGGATTGTGAGTGCAAGGCCAATCACAAGTTTTATCCATTTCCCCCCTCAG
Seq C2 exon
GTCCCAGGTCAAGTTCATGGGCCTGAGATGCTTGCCAGGGGTGTGGTGCCTCTGGATCCAGTTCAGGAGTCCTCAAGCTTCGACCATCATGAAGCTGCCCAGTCTCATTTCAAGCATTCGTCTAGAAAGCCTCGTCTCTTATCACCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001335:ENSRNOT00000045379:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.310 A=NA C2=0.843
Domain overlap (PFAM):
C1:
PF0202312=SCAN=PU(96.8=64.8)
A:
NA
C2:
PF0202312=SCAN=PD(1.1=2.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCAGGCGCTTCTGTTACCA
R:
GGCAGCTTCATGATGGTCGAA
Band lengths:
352-756
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]