RnoINT0143822 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23757520-23759269:+
Coord C1 exon
chr12:23757520-23757834
Coord A exon
chr12:23757835-23759191
Coord C2 exon
chr12:23759192-23759269
Length
1357 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
TGTTCTCTCTCCTGCTCTAGTTC
3' ss Score
9.82
Exon sequences
Seq C1 exon
GTGAGGGCAGCGTGCGCCTGGCGGGCGGTGCCAGCCCGTGTCAAGGCCGAGTGGAGATTCTGCACGGTGGCCTCTGGGGCACTGTATGCGACGATGACTGGGGGCTGCCGGATGCTGCTGTTGTGTGCCGCCAGCTGGGCTGTGGGGCCGCCTTGGCTGCCACCACTAACGCCTTTTTCGGCTACGGTACCGGGCATATCCTGCTGGACAACGTTCACTGCGAAGGCGGGGAGCCCCGCCTGGCAGCCTGCCAGAGCCTAGGCTGGGGCGTGCACAACTGCGGACACCACGAGGATGCTGGGGTGCTCTGTGCAG
Seq A exon
GTGCCAGGGGTAGCGGAGGCGGGGCCAGGCTAGAGAGGCGGGGCCTTTTGAAGGAGTTAAAGTGGGGAGGAGAACTGGAAGAAACAAAGGGCTGCGTGGGGACTGGGGTTTGGCTAACTATACTTTCCAAATTACCTGTACTCTCAGGCCTGCTCTGGGGAAGCAATTCAGATAACTCGTTCTCACATTCTCTGTAACTCTGTAGAATTATCACAGCATTCCTCTGTTACTAGGAATGGCTCCAGAATTGTCTAGAAATTTCCAGATATTCCTCACGACCGATTTCAGAATAAAGCAATATTTTAGAACTGTTCCCTCAAAGATTAACCCTGGCCAGCTGTCTGTAATCCTGATGATCTAATAATAGACTGCCCCACCCCCATCTGGACCCTCTCCAACTTGGGAGGTGTTTTCAGCAAATTAGGGGTAAACATTGGAGCAGAGCATGTAGCTTACCTGATAGGGCATTTACCTAGCATGCATGAGGCCCTGGGTCTAATGTCCAGCCTCACACAGTCTAGGCATACTGGTACATACTTATAGCTCTAGTACTCCCTGGGCTACATAAAACCCTGTGGTATCTGTGTCTCTATCTCCGCTCTTAGGGGACAATGGCAAGCTCATCTCTGTGAGTTCAAGGCCAGACAGGACTACTTAGTAAAACAGAATAGAGGTGATTTTTGTCTTGTTGAGGCAGGGTCTTGCTGTAGCCCAGGCTAGCCTCCCTAGTTGCAGGTATCACCAGTACTAGCCATCATACCCAGCCCAACAGATGGGTTATTGTTGCTCTTATATCTTGGGGAATTGAACCCAGAACTTTGTACATGTAAACTCTACCACTGTGCTAAATACACTCTTAGCCCAGCGAATAGGACTCATTGGGACCATTACACCATTTCTCAGGTAGACTCTGCTCTTTAGATGGAAAGTGTTTGTAGGAAACCAAAAGCCATCATTCCCAGCTTACAGATTGGAAAGTCGAGGTCCTGAGAGGTTCCAGGAGCCCTAGCAGAATCACAAGTGATCTTGTTCAATGAAGTTCATGCTCCCAGCCCTTTTTTTTTTTTTTTCCGGAGCTGGGGACTGAACCCAGGGCCTTGCGCTTGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCGCTCTGTCTCTTTCTATTTTGTACACACTAGACTTCTAAGAACGTTGGACACAAATGAAAACATGCATGTGTATCTGTGTACCTCACATAAAGGACTACGGTCAAGCTGGGCAGGGCTCACTGTATTCTAGCCCTTGGTGTACAATTTGTTCTCTCTTGGGAGACACTCTTAGCCCTGTGACTGACCCTTCTGTTCTCTCTCCTGCTCTAG
Seq C2 exon
TTCTGAGCCCTCCAACTTCCACAGCACTGCCTCCCTCTGTCACCAAAGAAGACTGGGCATGGCACACTGAGCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.333
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5)
A:
NA
C2:
NO
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:
TGTCAAGGCCGAGTGGAGATT
R:
GTGCCATGCCCAGTCTTCTTT
Band lengths:
342-1699
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]