RnoINT0142949 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92288685-92290586:+
Coord C1 exon
chr13:92288685-92288777
Coord A exon
chr13:92288778-92290448
Coord C2 exon
chr13:92290449-92290586
Length
1671 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATTTGTTTATTTTCTCCCAGCAA
3' ss Score
6.66
Exon sequences
Seq C1 exon
GCCCTTCTCAAAAAGCATGAGGCCTTCCTGGTGGACCTCAACGCATTTGGAAACAGCATAAAGGCTCTGGGGGATCAGGCAGAGGCCTGCCAG
Seq A exon
GTGAGAAGGATGGGGTTCTGACAGTAGTCCCACTTCTTAGTATAGGTGCAAAGGAATTCTGTTCCTGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCACAAACTAGAAACCAAGTGCCATGAAAATACTATTTCTCTTATTAATTTTTAGGTAAGAATGCTAAACTCTTTGTAGCATCTTCAATGGTGTATGCCAGAATAAATTTTCAATAAACATTAGGGTTTTTTTAAAAGATACTTTTGGGCTTTTTTATTTTCTCCTTGTTATTTCTTCCCTCTTACATCCATACTTTTCATATTTTTATCCTTTTAATTTCTTTGCTTTGTGACTTGGCTGTTATGAAAACATCAGGATTCATCAAACAGAGATATACAGGTTTCGATTAAAATAATCATGTCAGAAAATTAGTTGCTTACAGGGCTAGAAATATTTTTAAATGCCTATGTAACGCATGTATAAGAAGAAAATGGGACCACTATAAAAAGAAATTTCTTTCCTTCTGAAATGAATGTCAGAAAAGAGAAACAATTTCATAATAAAGACATAAAAAGTGCATTTTAAAAGCCCACAATCCATGGAAACAGATGGGCCACAGCACAGAACAACCAAGTATATTTGGGAAATCAGAAACCTGTTTGGCTGAGAGTGTTGGAAGGATGAGAAGTGGGTGATCAAGAATGATTACATTGAAATTAAGTAAGTGATAAAGTATCTTGTGTACAGGGGAAGAAGCAAAAGACGATATGTCTTTTTCTATTTAAGGAATCATTCTAATAAGCAATTAAGAATCCCCATGCTCAGTCTAGAACAGACTAAGCATGGCAAGTCAACAGAGGCTCACAGAATGCCTGTTTGTCTCTGTATCAGGCTGTGCCCAGCGGGTCCCTGGACACAGCCAAACTGATGCATCATAGGTCGAGAAGCAATACAACATGTGACAGGCATAAGTGAGAGGCAGAAGAGAAGGTTTCATCCTCTGTACCTGAATGGTGTGTACTTTGAAAACAAAAACAAAACTTTACAGAACTTAAAAAAAGAATGCTTATCCCAGAACAGAGTGATTTCTTTAAAGAGAAATGCATCTTAGTAGTATGCTCACAGTTGTTTGAATTCAGTTGTTTCTTCTGTGCTATAGGTTGTAAGTCTCTAAAGTACTAATTTCACAATCCCTTAACAAAATGAATTAAAGAGAACTCAGATGAGAAAACTTGTTATTTGAGGTCCGGAGAAAGGAGAAAGTGACAACAGATGGCCAACCTCATGTGCTCTGGTTCCTGAAATGTTGACAAGTGTGGTCCATTTGAATCTTCACAGAGAAGTATATTACCCTTCCCACTAAAGAACAATACCTTGGAACACTAAATGCTTCTGATAGTATCTGCATGTGCTGTTGGCCATGCCCATACTTTCCAATCTGCCAGGTCTCTGATAGGTTCTTCTGGCACAGCATCCTGGAGGATCGCCACTGTCTGACATAGCATCCATATCAGACCTCCAGCCAAGGCCCTGGGAACTGTGCACCAATGGTGAGCTCTACTTGGAAAGACTTTCAGGGTACAACTGACATCTGATTTGTTTATTTTCTCCCAG
Seq C2 exon
CAACAACAGGCAGCACCAGTGGATGAGGCTGGTCGAGAAGCTAGGGTCATAGCTCTGTATGACTTTGAGGCTCGCAGCCGTAGAGAGGTCAGCATGAAGAAGAATGATGTCTTAACTCTGCTCAGTTCCATCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(34.9=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.8=37.0),PF0001823=SH3_1=PU(63.0=63.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTTCTCAAAAAGCATGAGG
R:
TTGTTGATGGAACTGAGCAGAGT
Band lengths:
230-1901
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]