RnoINT0142980 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92338343-92340083:+
Coord C1 exon
chr13:92338343-92338487
Coord A exon
chr13:92338488-92339449
Coord C2 exon
chr13:92339450-92340083
Length
962 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TCTCTTCTCGTTCTTTTCAGGCT
3' ss Score
11.96
Exon sequences
Seq C1 exon
GAAAGGCTATGTGTCACTGGAGGACTACACATCATTCCTGATTGACAAGGAGTCAGAGAATATCAAGACAAGTGATGACATAGAGAGTGGATTCCAAGCCCTGGCAGAAGGCAAGGCCTACATTACCAAGGAGGACATGAAACAG
Seq A exon
GTGGGGTTCCACAGTTGCGTCTCCTGTTCTGACACTATAGTCTTGGTTTGGGTCATCTTGGTCTTGGCTCTCCTCTAGTACTCCCACCCATATACCCACTGAATTGCCTGAGGCCTCCTCTTTCACAAGGCATCCCTTGTTTCATTTAAATTGTTTGCTTTTACTACTCTAGCCCCAAAATGTCTAATGGTTCTCTACTGACTATTACAGCCTGTTCAAAATCTGCCACTCAATTTTTAAGCAGCTTATTGTCATTTCTACTGAATAAGACAAATAGAAAGAGCTAATTTCTCAATGTTTGTCAACTGTTGAATAGTAAAAAGTGAAAATGTATGTATATATATATATATATATACATGTATATTGTGCCATAATGAAAAACAGGGAACTTTCAAGAAAATTGGCAAAACTAGAAATTATTTCTAGGACTCAAAAAGCAATATACTGTACATTCTCTCTTACACTGGGACCCTAGATAATGATGGTTGTGTGCATGTATATAGGTGAGTATAGGCCAAGGAACTAGAAGGAGAACAAGAAGGGAAAAGAGGGTTTGAAGGGGTCATGGGAACTAACAAAACACATGTGACATGTACGATGGAAGACGACTGTTGGGGATGGGAGCATACAGAACAGGAAGAGAGGTGGGGGAAAGAATGGGGGATGGAGAGATCAACAAAATCAAATTGTGTTTGAAATGCCATAATAATGCAAAGATACGGACTTGTTGGGTTTGGTTTTTATCAAAAATATCTAAAGAAAAGGATATGAAAAAAGACTTGGGAAGAAATTTTTAATTAATTTTATTTTATTGGATGAAATAAATTTATGAAAAATTGGAGTGATAGGAAGAAGGCTGCTTCTCCTGATGGCTCTCCTTCTGTGTTTGCACAGATAGGGAGACCCATAGAAATAAGTGTTTGATTTCTGTAACTCTGTCTTTCTCTTCTCGTTCTTTTCAG
Seq C2 exon
GCTCTAACCCCAGAACAAGTGTCATTCTGTACCATACATATGCAGCAATATATGGACCCGCGGGGTCGGAGCCAACCTGCTGGCTACGACTATGTTGGCTTCACCAATTCATTCTTTGGCAACTGATAGGCAGATTCTTATGTACCATAGAAGATCATAGTGTGGCAACAAGTGATGGGAAAAAAGAGGCACAAACAAGTGTGAAAGAAAAATATTGCTCCTGGTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCCATTTATTGCAGGATTTAAAAATTTATCAAGTATATGGGCAGGAGTTCAAAAAATGCTATAAGATTATGTAACTAGTCTCTACTTAGGGTAGGAAGCTCTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCTGCACACCTTTAGTATTTTGCTGCATTTCTGATTATAGGATCAGTATTTTTAAAAATGAAATTTAACTAGAGTTATGCTTTTGTATTTTCAGAACCATTATTATTACTAAGTATAAGCTGTTAATTATACTGTGAAAAGTACAATAATAAAGTAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(20.6=26.5),PF087265=EFhand_Ca_insen=PU(40.6=57.1)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(56.5=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTCCAAGCCCTGGCAGAAG
R:
ACACACACACACACACAGCAG
Band lengths:
357-1319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]