RnoINT0142966 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92304348-92306276:+
Coord C1 exon
chr13:92304348-92304556
Coord A exon
chr13:92304557-92306155
Coord C2 exon
chr13:92306156-92306276
Length
1599 bp
Sequences
Splice sites
5' ss Seq
AGAGTACGT
5' ss Score
6.58
3' ss Seq
ACTTTCTTCCTGGGTCCCAGGGA
3' ss Score
7.66
Exon sequences
Seq C1 exon
GACCCTCTCAAAGATCTGAATGGTCTGGCTAAGGAGCTGATCTCCAGTGGGACTTTCAACATTGAGCAGATAGAAGAGAAAATGAATGGTGTCAATGAGCGTTTCAAAAATGTCCAGAGTTTGGCAGCTGCACACCATGAGAAACTGAAAGAGACCTATGCCTTATTCCAGTTCTTCCAAGACCTGGATGATGAGGAAGCCTGGATAGA
Seq A exon
GTACGTATCACTCACTGGATAATTCACCAAACAGATTCAATCCTTGCTGAAGTCAATTTGTAATATTTTTATGTTGATTAAACTTTTAAACCTCTTCCTTGACTGAAAGTAAGCATTGATTCCACTTTTTAACTTTCAATGGATACAGGCAGGAAACCAAGGGCAGAGGGAGATATGAACAGGTCAACCACATTCTGAGAATAAAATTCAAACACCATACACATTTTTCAAAATAGTTCACTTAATTATAGCACACGGAAAGCTGACCCTTTGCAACTAATGCAGAAGACCACAACATGGTCATAATTATTTACTTTTTAAAGGTATATTTGTTTTTATTTATGTGCTCATGAGTATGTCTGTGTATATGTGTGCTTTCATGCAAGTGACCATGGAGGCTAGAAGAGAACATACAGTCCCCTAGAGCTAGAGTTGTAGATTTGCTGTTGAGCCTCCTGATATGGGTGTTAGGAATCCCAAACTGCAGTCTTCTACAAGAGAAGTAAGTACTCTTAACCAATGACACACCTCTCCAGCCCAAAACCATTACTCTTTCTATACTTGTCGCATTATATATAATGATAGGTAGCCCCTGTCATAGTTTCAATATTGACCCCATTCTTTTAAATATGGGTGTGAAATTCTTAACAAATCGGTAGTTTTTGCCTGTTTCATTGTTACTTTGTTCCTTTTGTTTCTCAAATTCCAATCTGCAGATTCTTACAAGTTGCACATAAATTAGAAGGAAGTGTTTTATAAGGTGTCAAATAGGACCTTTCAGTAGTCATAAAATACCATAACCTTTTGGTGTTCAAAATTTTTCATGTAGTTTGTAACAGTAAAGATCAAACTCAAGACTTTTTACAAGCTAGGCAAGTTTTCTACCACTAAACTATATCCCTACATATTGTTATTGATATTAATACACAAAATAATAAAATTCATATAATTTTCATAGTTTTAAAAATGAAATATTAATACATGTACTAGAGTACTAATGGGAAGACTGTTACAATATATACAAGCTGGACATTAGTGTGTTATTTTCATTTTTGTTGACATAAAACAAATTTTCTAAAATTCTCTTCCACTGCTTATCTTTTTGTTGGTTCCTTGATCAGTAAGGGGCTTGTTATTGTTATAAAACATCCTGACCTAAACAACTTGGGGAGGAAAGGGTTTATTTCAGTTTACAGTTCAACAGTACAGTCTTTTACTGAGAGAAGACAGGGCAGGAACTGAAACAGGCCAGGAACTTGGTGGTAGGAGCTGATGGCAAAGACCATGGGGGGAGTCCTGCTTACTGGCTTATTCCTCATGGCCCACAGTGAACTAGATCCTCCTACAACAATCAGCAATTAAGAAAACTCACCACAAGCTTGTCACTGGGTCATTGCTGTGGGGGCATTTTTTCACTTGAGTTTCCGTCTTCCCAACAATTCTAGTTTGTGTCAAGTTGTCATAAAACTAGCAAGCATGGTCCCAAAGTTCTTCGGAATCTGCCCACTCTCACTACACATACACGCAGAAAGCTATCATACTAGTTTCTGCTTAGATATATCTAACCTCTGATTTTCCCACTTTCTTCCTGGGTCCCAG
Seq C2 exon
GGAGAAGTTGCTACGAGTGAGCTCCCAGGACTGTGGGAGGGATCTTCAGAGTGTTCAGAACTTACTGAAAAAACACAGACGCCTAGAGGGGGAGCTGGTGGCACATGAACCTGCTGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(47.6=71.4),PF0043516=Spectrin=PU(16.2=24.3)
A:
NA
C2:
PF0043516=Spectrin=FE(38.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCTCTCAAAGATCTGAATGGT
R:
CTGGACAGCAGGTTCATGTGC
Band lengths:
329-1928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]