RnoINT0142998 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8567678-8568967:+
Coord C1 exon
chr3:8567678-8567770
Coord A exon
chr3:8567771-8568832
Coord C2 exon
chr3:8568833-8568967
Length
1062 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGC
5' ss Score
7.73
3' ss Seq
CCTTTCCTTTGGACCGTTAGCAA
3' ss Score
2.62
Exon sequences
Seq C1 exon
GCTCTGCTCAAGAAGCATGAAGCTTTGATGTCCGATCTCAGTGCCTACGGCAGCAGCATTCAAGCTTTGCGAGAGCAGGCTCAGTCATGCCGG
Seq A exon
GTATGCAGTGCTACGGGAGTTCTAAGGGACTGAGGGCAGAGATGGGCTAAAGAAACTGATGGACATGTGGGGTGGGGGGTAACATTCTTTGGGTTTGTTTCTTTATGACAGGGTCTCACAGTGTAAATGAGGCTGGCCACCTCCCTCCAGGTTGTTCAAGTGTTGGAATGCTGGGATTAAAGGTTCAAACCACCATATGTGCCCTAGGCAACATTCTTCTTATACAAAGGTCCATTGTCGGCACACTTGAGAGTTTTTGTTTGATTGAACCCCCGCCTTTTGATATTTTAATAAGGGGGTCTCACTTTGTAGTCCAAACAGGTCTCAAGCTAATTAATCCTTCTCTTTTGCCTTCTCTAGTGCTTGATTTATAACTTTGAGCCACTATACCTGTATTATTGAGTAAGAGTAACACATTTGTTCGACAGCTTGAACAAATATTTTTTTCTGGTAGCTTCAGTAAAAAGCTCTCAAGCGGTTGTGTGTAACCAGTGCAAACATTTAATTCCAGCACTCAGCCCTCAGGAAGCAGAGACAGCTGGATCTCAAGGCTAGCCTGGTGTATGTAGTTCTAACCACTAGAACTGAGCTGGCTCTTTACGAAGCTCTGTTTCGGCTCTAAGGCCATAGCTGGCTGGTGGTGGAACACACTGTTTATCCCAGCACTTGAGAGGCAAAAGCAGGCAGATCTCTGTGAGTTCCAGGCTACACAGAGAAACCTTGTCTTAGAAAAAAAAAACCTCTTATAAGTGTGTATTCGAAGACGCCAGTCGAACGTTGGCCTGTTGGGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACCGACTGCTCTTCCAGAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGAATCCAATGCCCTCTTCTGGTGTGTTTGAAGAGAGTGACAGTGTACTCATATACAAAATAAATAAATAAATCTTTAAAAAAAAAAAAGAAAGAAAAAAGAAAGTTGGCCTGTTGTGTGCTTGAGTGATAGATGGCATTTAATCATTTTCCCTTTCCTTTGGACCGTTAG
Seq C2 exon
CAACAAGTGGCCCCCATGGATGATGAGACTGGCAAGGAGCTGGTCTTGGCTCTCTATGACTATCAAGAGAAGAGCCCTCGTGAGGTCACCATGAAGAAAGGGGATATCCTCACCTTGCTCAACAGCACAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.179 A=NA C2=0.181
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(35.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(17.9=33.3),PF0001823=SH3_1=PU(63.0=64.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATGAAGCTTTGATGTCCGA
R:
GCTGTTGAGCAAGGTGAGGAT
Band lengths:
205-1267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]