RnoINT0143821 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23756910-23757834:+
Coord C1 exon
chr12:23756910-23756987
Coord A exon
chr12:23756988-23757519
Coord C2 exon
chr12:23757520-23757834
Length
532 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
TCTCCATCCACCATCACCAGGTG
3' ss Score
7.58
Exon sequences
Seq C1 exon
AATTCTTGCATACACAGCCCCCAGCAAGGAAGGTGTTGACCAGTATAGCGCCCCCTACAGCCCTCCAAAATGGGAGAG
Seq A exon
GTAAGTGATATGGCAGTCGGGCCCTTGGTGTAGGCTAGAGGAGCTGAGGGAAGTGGGGGTTGAGGGCTTCAAGGTCATACCCGCAATGTACAACAAGGACCCTCTTTTGAGGGACATGGAGAGGGAGGAAGCTTAGAGGAGGCAGGTCCCATGTGTCAGGAGTGGGGGAGGGCTTCATGGAAGAAGAGGCGTGGCAGCTACATCTTACGAAGTGAGGTTTTCTCTGGGCAGCTGTACATGACAAACAGGCACATTTTACAAAGCAAGGACAAGAAAGGGAAGGCTAGTTTTTAGGTCAGGATGACATAATCTACTCTGGTTATCCTGAGACCCACAATCCAACTTTCTGGACTGTCAGAAGGCTCGGCCAAGGGGGTGGGCTGGCTAGCTTATCCCTGCTGTGGGGTTTTGGTCATGCAGCTGAGGTTGCTGTCCCAGGGAAGGCCCGGTACATTAATGAAGTAGATGAAAACGCCTCCTCATGGCCCTGTAAAATGCTACTTGCCCTACCCTCTCCATCCACCATCACCAG
Seq C2 exon
GTGAGGGCAGCGTGCGCCTGGCGGGCGGTGCCAGCCCGTGTCAAGGCCGAGTGGAGATTCTGCACGGTGGCCTCTGGGGCACTGTATGCGACGATGACTGGGGGCTGCCGGATGCTGCTGTTGTGTGCCGCCAGCTGGGCTGTGGGGCCGCCTTGGCTGCCACCACTAACGCCTTTTTCGGCTACGGTACCGGGCATATCCTGCTGGACAACGTTCACTGCGAAGGCGGGGAGCCCCGCCTGGCAGCCTGCCAGAGCCTAGGCTGGGGCGTGCACAACTGCGGACACCACGAGGATGCTGGGGTGCTCTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=0.019
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTGACCAGTATAGCGCCC
R:
CACAGAGCACCCCAGCATC
Band lengths:
358-890
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]