RnoINT0143839 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72452030-72455595:-
Coord C1 exon
chr1:72455278-72455595
Coord A exon
chr1:72452594-72455277
Coord C2 exon
chr1:72452030-72452593
Length
2684 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
CCTCCCTCCCGGCCTCCTAGGGA
3' ss Score
8.98
Exon sequences
Seq C1 exon
GGTCCCCCCAGTTGCGCCTGGTGGCTGGACCCAGCAGGTGCTCTGGTCGGCTGGAGGTATGGCATGATGGACGCTGGGGGACAGTATGTGATGACAGCTGGGACATGAGAGACTCAGCTGTGGTCTGCCGGGAGCTGGGCTGTGGGGGGCCCCGACAGCCAGACCCTGCAGCAGGCCGCTTTGGCTGGGGCGCAGGCCCCATCTGGCTGGATGATGTAGGTTGTGTGGGGACGGAGGCTTCACTGTCAGAATGCCCTGCTGCTTCCTGGGGGAAACACAATTGCGCCCACAATGAGGATGTCGGGGTTACCTGCACCG
Seq A exon
GTGAGGACGTGCTAGCTATCCACTGGCTCTAGGAGGGCTTCTCAGAGGAAGGCATGGAGGCTAAGGGTGGCGATAACTTGACTACTGCAAGTCCCCACTCTGTGGTGCATATTTAGCTCATACAACCTTATTGACATCGCCTATGTCTACCCAAAGTGAGGGCTACTTCCCATCAAGGCTGGCAGTGCACTTCCCCCCATTTATAGGGGTCTGGTTTCCAACCTCAGTGGTAGATGCTAAGCTAGGAGTTGGGTGCTCAATAGGACGGGGCTGTGAGACGCTCAGGCCTCGTGGAGGGCAAGGGGAACACAGGTCAGCTATTGCAAACCAGCAGGACGAGGTAGTGTTTGGGAGGCCTCTGAAACCGCACTGAGGGTCCTTCTGTTGCTAAAGGACTCTCGGAAGTAAGAGGCTCGGTGCTATATTTCAGTATAGTGAAGATGCAGGTTAAGTTAAACCAAGGGAAACACACAGGGAGCGGCGTTTGGGTGTGAAGTGCTGGTGGTGTAGACAGTTCTGCATTATCCCAGCAACCTGTGTGACGACATACAAGAACAGCCATCCAGACATGCTAGCCTCGAGGTCTGCAGGTTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTCTGACAGGGCCTTGATTGACCATGCACGTGGCTGTTCGGAAGTCACATTGTCAGTATGGACTTAAGATGGTGCGAGTGTCCTCTTCTCTCTGCCCCAAACACATAGTTTCTTACCAGGCAAGAACATTCCAAGGGTGTAGAGGTCATCCTCCTGGAGCCAGGGGCAAAGTCCCCAAGCTTGTCTTAGGCATGGCTCATCCTTGATTGCCTAGGTGACCTAACCAGAGAGACAGAGTGTGGATATTGGTGACTCAAAGGATGGAGTCATCAGCTCTGCCTCTGTCTCTTCTGGGAGCCACGGGAGGAGGGGGAGCAGGGAACGGGCATGTAGGCTTCATGCCACTTTCGAGGGTAATAAATATGAAAGAAAAGGCAGGGACAAGAGAACATGCCTGTAGTGCCAGCACTTCAAAGGCTGAGGCAGGAGAAGTCTTATGAATTTAAGGCTAGCCTGGGCTATAGTAACCTTGTCATGGAAAAAAAAAAAAACCCACGAAATGAACAAGGGCTAAGTGGTTAAAAGCGCTGGCTGCTCTTGTAGAGGACCCAGGTTTGATTCCCAGCACCCACACGGCAGCTCCCTAACGCCGCTTGGTGGGTGAGGATCTGATTCCCTCTTCTGGCCTCTGCAGGCACTGAACACACATGGTGCACAGACATATGTGCAGGGAAAATACATCGAATAGAAATAAATCTGTAGTGTGTGTAGGGTTCGGGTGAGGAAAGAAAGCAAGGCCTGGTGGCACAGTCCTATAATCCCAGCTATTTGAGATGATGTAAGAGGATCACAAGTTCAAGGCCTGCCTGGGCAGCTGTGCCCCTGTCTCAAACAGTAGAAACATAAGCAGGTGTTAAAATAAGAGATGAGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGCTCGGTCCCCAGCTCCGAAAAAAAGAAAAGGAAAAAAAAAAAAGAGAGAGATGAAGGCCTTAAGGCAGTGGTTCTCAACCCATGGGTCGTGATCCCTTTGAGTGTTCAATGACCTTTTCACAGGGGTCATTTAAGACCATTCGAATAATCAGATATTTACATCATGACTCATAATAGTAGTAATATTACAGTTACAAAGTAACAACAAAAATGATTTTATGTCTGGGGGCCACCACAACACGAGGAGCTGCATTAAAGGGTCACAGCATTGGGAAGGTTGAGAACCACTGCCTGAGGGTGTGTGCCTAGGAGTGGAATAGCTATCCTGAGTTGCCCTCTTCCTTGCCTTAAAAAAAATACTGATTTTATTATTTTAAATCATGTACACGCTTTTGTTTGTGTATCGTTCTTCCCTGCTGAACTGTCTCCCCAGTTCCTTATTCCCAGCTCTTTGTGGAATCTGCACACTAGCTTCCCGGAGTGGCTACACCACTAGACACTCCCACTAAGGGTGAATGAGGACTCCATCTTGTCCACTGGCTGTCATTTGTCTCCTTGATGATGGTCCTTCTGACTGGGATGAGATGGGCTCTCAAAGTAGTTTTAACTGTTGCACCGGGCACTTAATGGCAGTTTCAATCCAGTGGTAATGCAGGTGGCCTTTGCTGGAATTAAGTGGGTCACGTGACAAAACCCAAGGCTATGAAGTGGGGAGAGGGTCAGATAGGGATGAGAGAGATAAGAGAGGGCAATTAGGGAATGATGCATTATAGGCATGCTCGCAATGGTCAGGAGACAAACACACCTAGTATAGACTGCCTTTACTTAGCTGTTTCTGTGGGGGTGGGGTATTTTGCCTGCAAGCACCATGTGACTGGAGCCCTCAGAGGCCAGGAGAGGCCATCGAATTCTCTGAGACTGGAGTTACAGCATCATTGTGTGTGTGCTAAGAATCAAACCCAGGACTTCTGAAAGAGCAGCAAGTACTCTTAGCCACGGATCCATTTCTTCAGTCCAACAGACTTCTATTTCCTTAAGGGAAAAGAGGGCGGAGGGTATGGGTTAGCGGTACAGGATGCGATCTTCCTTCATGATCTTATCTCTCCTCCCTCCCGGCCTCCTAG
Seq C2 exon
GGACCCCCGGCCTGGACACCATCTCAGACCCTTTCAGTTGGAGCTGGCTCCCTGGGCTGGGTAGAGATCAGGATGCCTGGCTCCCAGGAGAGCTGGCCACCAAGCCTTCTGCCAGTCTCACCTCCAGTGTGCTACAGAAAACCACAAAGGCTCCAGGGAAAGTGCCCAAGAGTACCAAGAAGTGGGTGACTAAAAATGCAAAGAGACCAACCACTCAGCCCCCTGGGATACCAATCACTAAACGCCCCAGGGTCCCAGGCACCCCAACCTCCCTAAGCCCAACCCCACGTACCTCTGAGTTACCAAAGAGACTTACTGCCGAGGCTCCTCGCAGACAGACCTCACACACCACCGAAAGGCTGACCCCTAGGGTCCCCTGGGAGTGGACCTCAGAGACCGCGGCATCACTGTCCACTCAAGGCCCCCAAGAAGTGACCTCTGAGGCCACCACCGCACAAACCCCTCAGACCTCCTTGGAGCCATTTGGTGAGAACCCAGAAGGCTCTCTAGAATCTTCCCAGGATCCAGCTGCCACCCCGACTGCTGGAGTTCCCGTGCCATCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.280 A=NA C2=0.894
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:
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]