RnoINT0142978 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92335894-92337660:+
Coord C1 exon
chr13:92335894-92336081
Coord A exon
chr13:92336082-92337513
Coord C2 exon
chr13:92337514-92337660
Length
1432 bp
Sequences
Splice sites
5' ss Seq
CAAGTACTG
5' ss Score
0.23
3' ss Seq
AAAATGCTTTTGGTCTTCAGACA
3' ss Score
5.17
Exon sequences
Seq C1 exon
AGGAAGCAGAAGGAGATTCAAGCAATGAAGCGTCATCTCACCAAGATTGAAGACCTGGGGGACAGCATGGAAGAGGCTTTGATCCTTGATATCAAATACAGCACCATTGGACTGGCCCAGCAGTGGGATCAGCTGCACCAGCTGGGGATGCGAATGCAGCACAATTTGGAGCAACAGATTCAAGCCAA
Seq A exon
GTACTGGTTTAAACCCAGGGCAGGGAATGGGCCAGATGGTATTGGATGTTGGAGTTTAATTAGGTTGGGCCTCAGGTCCCTGATAAAGAGCACTTTCAGAGATGGCTCATTTATCTGTCATATCAATCTCTCTTTTCTGTTCCACACCTGAGCTACTTTTTTTTATAGCAGGGTCCACTGTGAAATAAGCAATGTGCCCCTGCCTCTACATGTACACATCCTCTTTAAAGACACATGAGTCCTCCATTCAGGATCCTTTTAACATTTCATAATCTTTTCAGAAGCTACTCCCTTTTATAAAATTCCATTTAAGATATAATATCTAGAATGGAACATTTAAACTGTGGACTAATGAACCATAAAGGAACAAATTAATTTTCCTAAATAAATTAAACCTATAACAGCAGCTTTATGTCTCAATAGTCTTTGGAAGCATTTTTCTGTACATTAGAAATTGACAATCATCTTCTGTAAATTACCTTGTTATAAATAATTAAACCTTTTCAAACCATTAAATTTCGTTTGAAGCGTTGCAATTTTGCTAATGTACTGGAAAGCAGCCAAAGAAAATTTGTAACTGAATGAATATGGCTCTGCTCCAATAAAACTTTATTCATAGGCTTTGAAATTTGAATTTCATGTCTTTCATGACTCATAAAACATTTTTCGATTGTTTTCATCTATAAAGAAGTATTAAAACCATTCTTGTCACAGGAAGACAAGGTTTAGACTCAGGAAGTGGCTAGATTTGGTTCCTGGAGCATAACCTGATAACCTCTGAACTAGATAGATCAAATAATACATTAATATACAAATAATATATTAAAATTTTTTCTACCTTTTCTATGTCATGTTCATTGATACTTAACTGTTTTATTTCCAGAGGTAATTCATTTTTTTTCTTCCAGAGACACCATAGGTGTGAGTGAGGAGACACTGAAAGAATTTAGCACCACATATAAGTGAGTATAAGTTCACAGTTGGCTGGTCCTTTGCCTTCTAGAAAATTCATAATAAGTTTACAAATTTCTCTCTCTATGTTCCTTGATCAGACCTCAGTGACAATCTAGTCTATGTATGCAAATTATCACCAGTACTGGATTGCTGTAGCCAATTTTAATCATCTGTGAGATCCCTGGATTTTAAAAGTAAAACATGTCTTTAACACATCACTCAATTGGTGATTATGTTTGCTCCATGTAATTCAGCTGTTTCTGAGGGCAGAGCAGGAGAGAATAGTCAACGCTTTGTGTTATTCCTACTGTTACTGGATTTAACAAAAAAACACTCAGAGATACAGATAGACTTTCTTCTGTGTGTTCCAATAGTATTATGGCATGTCATTGAAGATGTAGTCAACATAGCAGAATTTGATCTTTTCTGTTTTAACCTGGTTCTCTCTTGAACTTGATAAAATGCTTTTGGTCTTCAG
Seq C2 exon
ACACTTCGATGAGAATTTGACAGGGCGATTGACTCACAAAGAGTTCCGGTCATGCCTGAGAGGACTCAACTACTATTTGCCTATGGTTGAGGAAGGTGAACCTGAGCCCAAGTTTGAGAAATTTCTGAATGCTGTGGATCCAGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.100
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(64.0=90.5),PF134991=EF-hand_7=PU(0.1=0.0)
A:
NA
C2:
PF134991=EF-hand_7=PU(77.8=98.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAGCAGAAGGAGATTCAAGC
R:
TCCCTGGATCCACAGCATTCA
Band lengths:
334-1766
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]