RnoINT0142958 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92299000-92300521:+
Coord C1 exon
chr13:92299000-92299197
Coord A exon
chr13:92299198-92300377
Coord C2 exon
chr13:92300378-92300521
Length
1180 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
ACCTACCCACCCCCTTATAGCTG
3' ss Score
8.15
Exon sequences
Seq C1 exon
GAGCATTATGATGACATAAAAAGAGAAGACCCCACTTTCCAAGCCTTAGAAGACTTTGGTAGAGAACTTATAGACAGAGGCCACCGTAATAGCCACGAAATTGAAACTACTCTCCAGGATATTAAATTAAAGAGAGACGATTTGGAAAAGAATTGGGAAAACCGCAAGAAGATGCTAGACCAGTGCCTAGAACTGCAG
Seq A exon
GTATAGCAGCTTCTGGAGAGTATGGGGTTAACCTCAGTTACCTGAGTATGGTTTTATATGCTGATTGGGGGCATTCACTGTATTAGACTGTGCGAGCTATAAACAGCAGTGTCTTGTGATTGTCTGACACTGTCCTCGGGGTTATAGACTGAACATCCCTGTGCTCTGTGGTTTTGTTCTCATTAAAGGAGATGAAAAGTGGCAGTGAAATGGTCCAGTAGGCAAAGAAATTTGCTGAAAAAAGTGTGATGACCTTTTATTCTAGAATACAGGTAGAGAAGAAAGCCTACTTCACGAAATTTTTCACTGACTTTCACATGCACACCATAGACCTTCCCCTCACACACATCCTCTCTTTCATCCACAGACAGGCAACACATGCTACTAAAAAAAAAATAAAGTTTTAAAATTTAAGAGCTTTTTAAAAGGAGAGATCAAAACAAGATTATAATCAGTCTTGTACATAAATGGGATTATTGTCACTAATTATCATTAAATAATTAACTAAATGATTAGTTTTTATTAAGAATAGCATTGTACAGGTCACAATACTACAAATATCATTAGAATATGTTTATATAAGAAGTACAGATCATTCTAATATAGGAGATGTTTACTAACTGAATATATGAATGATTTGAGGATAAAGAGGAAAGCATGATCATGGTGTCTGAGGAAAGAATATGGGTGTGTCACACAAGTCTATGGATAATATTTTTCAAAGTTTTAAAGAAGTAACCATTGAAAACCAAACATATCTGTAATATTAGAACTTAAATTTGTAGTTCGTGGTTATCTCCTGTTGCATAATGAATTTGTTGCTGTTGTAAGCTAGCCAAGACTGTCTCAAGTTTTGAGGGGGAGGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACTAAACAAGTTAGTATCTACTAGATGTACCATATAGAGACAGCGTTTTCATATTTACTATAGCTTATAAAACACATGGTAGGTTTGAAACAAAAATGATGGTGACAATGTACTTGAGATTCATTATGAGAATGCTTTGAGAGAGACTGTAACAGCCCCGGCAAGTTGTTTTATGTCATCCCCAATGAGGGATAAGATCATTTCCTTGGTTCATCTAGAATTACCTCATATCTGCCTCTGATATTACCTACCCACCCCCTTATAG
Seq C2 exon
CTGTTCCGAGGGAAGTGTGAACAGGTTGAGAGCTGGATGGTGGCACGTGAGAATTCCCTGAGGTCAGATGACAGGGATCACTTAAACAGTCTACAGGCTTTGATGAAAAAACGGGATGACCTGGACAAAGCAATCGCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.136 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.2=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:
TGATGACATAAAAAGAGAAGACCCCA
R:
GCGATTGCTTTGTCCAGGTCA
Band lengths:
327-1507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]