RnoINT0142977 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92333965-92336081:+
Coord C1 exon
chr13:92333965-92333995
Coord A exon
chr13:92333996-92335893
Coord C2 exon
chr13:92335894-92336081
Length
1898 bp
Sequences
Splice sites
5' ss Seq
TCAGTAATT
5' ss Score
0.5
3' ss Seq
TTGACTGCCTCTTTTCCCAGAGG
3' ss Score
8.67
Exon sequences
Seq C1 exon
GGCTTATTTTCTGGATGGGTCAGTATTTTCA
Seq A exon
GTAATTATGTTTGTCTTGTTTTTAATGTTGTCCTAGAGTAATTAGTTAAGAAAACTTTAGGGCCAATATATCACATCTCATCAAAATCTACTAGGCCTAATTAATGATGTGGGGCGAGAATAAGGATTCATATTTTCTTCCAGCCCTGAACTCATACTACTGAATGTAGTGTAACTATAATGCGATGCACTGTTCCTGTATTACATGACTGTCATGCACTGCACCATTCCAGTGATGACTGTAAAGGATGGAAAACGTGGGAAAAAAGACTAAACCCTAGTAGTTCTTCCCAAAATAACGAGTGGTACCTCCCTCACATGTTAAATGTATAGAATAAAATCTGAAAATTCATGAGCAGTATTTCTATATGTCCAACCAATTATGGGCTGAAAATATTCAAAAAAATTATCTTTCCCGAATATATAAATATTTTTGTCATCATTCTCTTTAAAGTTCCTAACAACTATTTGCATCATATTGGGTATTATAAGCAGCCTAGACTATAATATGCACATACTGCATGCCACGTTTACATTTTGTAACTGCAACTTCTACTATGTTAGTAACCATAAAGACACCTATGGACACCAATAAATAGTCACCTTTGAGAGTAAAACTAAGGAAGATGTGTGACTCCTTCTAGAAAGAGTAGAACTAAATCTGGCTTTATGTTCCTTTTTATCTATCTAGAAAGATTGACAGAAAAATTGTTCATTAAAATTTGGCTTCATGAAACTTTATTAAGTCCATGTAACTTGGGAGAAGTAAAAACAATGAACTGCAGAAAGTTTGAGCTAACAGGTCTGTGAAATATAGATTTCCGTTACAACAAATAATGTTTTCTTTTGATTCTTAATTAGATCGTTGCTCAAGGAAACAGGAACTCTGGAATCCCAACTTGAAGCAAATAAAGTAAGTGATGTTTGTTCACTAGCTGAAAAAACTGCTTGAAATTTAAAAAGCACAAGGGAAAGCACTTAGAGGCAGCCTGGTGATGCTTTACATAGACGTTACCCAAGGTCAAGAAGCCAAGGTTGTAGTCCTACTCAGATGTCAATTTGCAATGTCACTTCAGAGCATGTCATTATACAGGCCCCAGTTTACTTAATTTTTTAAGTGTCAGTTTTTACAACAGTATATCTAATAAATACATTAAAGGTTTCTGATGTGCTTAACTAAAAAAGCAGATACACATGTTCCTAGGCTATACCTGGCAGAATCAATGAATTTCTCTTATTAGATATAGGCAAGTATTATAACTGAATGCAGATCCTCTCCTGTCAACTGAGGGAAACAGTGGGCTAAAGAGCATTTCTTAGTCTTGTTTGCATTATTGTCTTTTTCTAAGAATAAAAAATAATTAGTTCAATATACATTTTCCCTAATGAGAAAAGAATAAGATGTCAGGTAGAACTAATCTACTCCATAACATCGAAGTTTTTCACCTGTCTCTCAGAGCTACTTTGCCCATTGACTCAAGATGCACATTTCCCCTTTGTCAGAATGCTTTGGAAAAATGTAGACTTTTTTACATATGTATACTGTTGCTTAGATATTGACAGTAGCCCATCATCCCTGGTGGTGAAGGAATATTGGAAGTGAGCACACTGAGGCTATTGGACGAGTCAGAGAACTAATTCCTAGTGAATGGAGATAATTCACAGCGTAATAACTGGAGCTGGTGGGGTCTGAGGTACAGGATGACAAGCATCATTCACACAGATATTCTGCTCTTTTTCAAAGGGAGGATTAAGGAAGGAAAATAGTTTTCCTGAGTTGTTCTTGTTATAAAGAGGATAGAAAGGCCTTTAAAAATGAACAAATTAGGGAAAGTCAGTGTCTTATCTCCTATCTCTTGGGTTGTAACTGGTGGTTTGATTGACTGCCTCTTTTCCCAG
Seq C2 exon
AGGAAGCAGAAGGAGATTCAAGCAATGAAGCGTCATCTCACCAAGATTGAAGACCTGGGGGACAGCATGGAAGAGGCTTTGATCCTTGATATCAAATACAGCACCATTGGACTGGCCCAGCAGTGGGATCAGCTGCACCAGCTGGGGATGCGAATGCAGCACAATTTGGAGCAACAGATTCAAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:46
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=0.016
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(11.2=100)
A:
NA
C2:
PF0043516=Spectrin=PD(64.0=90.5),PF134991=EF-hand_7=PU(0.1=0.0)
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:
GGCTTATTTTCTGGATGGGTCAGT
R:
TGGCTTGAATCTGTTGCTCCA
Band lengths:
218-2116
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]