RnoINT0143036 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8598480-8599258:+
Coord C1 exon
chr3:8598480-8598627
Coord A exon
chr3:8598628-8598791
Coord C2 exon
chr3:8598792-8599258
Length
164 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TACCATCATCTCCCCACCAGAAC
3' ss Score
7.59
Exon sequences
Seq C1 exon
GGACGGCCACGTCTCCCTGCAAGAGTACATGGCTTTCATGATCAGCCGTGAAACCGAGAATGTCAAGTCCAGTGAAGAGATCGAGAGTGCTTTCCGGGCCCTCAGCTCCGAGGGCAAGCCTTATGTGACCAAGGAGGAGCTCTACCAG
Seq A exon
GTAGGGCTGGGGAAGGGCAACATTCCTTGGGCACAGCTGGTGCTGAAGGGTACACCACACACACAGACTCAGAGGCCTGAGTCTGCTGGCAACTCCTTCCCTGTGGGCACCTAAGGTCAGCCCTGGTGGATCTGACCGTGACTGTACCATCATCTCCCCACCAG
Seq C2 exon
AACCTGACCCGGGAACAAGCTGACTACTGTGTCTCCCACATGAAGCCCTATGTGGATGGCAAGGGCCGCGAACTTCCAACTGCCTTCGACTACGTGGAGTTCACCCGCTCTCTCTTTGTGAATTGATCAATCCTCTTGGCTTCCAGACAGCCTGACCCACATGCTTGCCCTGCTATCTGTCACCTTTGCTGCATGTCACTCCCTCTGCTTTCAAGGACAATATTCCAGACAGCGCTACTTTCCAGTGTAACCATAGCCTGCTTAGCTTGGGGTAAGACTTAGTAGAAAATGGTGCTTCAGTAAACCGCTTACTTCCAGTCACAATCACCTTGTTGCTGTGGGACCCGACCCTGTTTGAGCCGGCTGCCCTCATTCCCACTTAAATCAAAGCAGCTGGCTAGTCCCCCTGTTTCCTTCCCAAATCCTGTTTTCATGTACAAGACAAAATAAAGGACTCAATTCTCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:55
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(17.3=26.0),PF087265=EFhand_Ca_insen=PU(41.4=58.0)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(55.7=92.9)
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:
GAGGGCAAGCCTTATGTGACC
R:
AGGGAGTGACATGCAGCAAAG
Band lengths:
243-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]