RnoINT0138516 @ rn6
Intron Retention
Gene
ENSRNOG00000010378 | Slc4a5
Description
solute carrier family 4 member 5 [Source:RGD Symbol;Acc:1303009]
Coordinates
chr4:114962510-114964349:+
Coord C1 exon
chr4:114962510-114962597
Coord A exon
chr4:114962598-114964194
Coord C2 exon
chr4:114964195-114964349
Length
1597 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
CCCTCCCCATTCCTCACCAGCTC
3' ss Score
7.18
Exon sequences
Seq C1 exon
ATTTCTGTTCATACTTCTAGGACCTTCTGGAAGAGCAAAGTCCTACAATGAGATTGGCCGAGCCATTGCAACCCTCATGGTGGATGAT
Seq A exon
GTAAGTGGAAATGTGAGGCACCCACTCCTTTCTGAGTGCTAATGGCTCTGCACTGGCACAGCCATCCCCACTCTGTCATCACTAATCATCTCACAAGCGCATCTGAACCCCTGCTGTGCACCGGGCCTGAGGATTATGAGATTCAGAGAGTAGGACCAGACTCTCTCATTTAGGGGCACTATCCAGGGAGAGGGACAGATCTGCAATAATGAGATAATAAAAAATAAAATTAACCATGTGCTTGCTATCTGCCTGGGAAACCAAGGCAGGCTCTGCAGATAAAATACTCAGGGTGAACAGGAGGCGGGTAAATTAGCATGGCCTTGAGATGCTAGACTTCCGGAAGCTAATGGAAGTGCAGTAGGGTAAGTTCAATGTAAGAGCTCCCCCAAGGCAAGAGCGGTGACTTGAGCCGGAGACTATATATACCCTGGGACAAGAGCCTAAAGGTCCTGTTCTGTCCCCAGAGTGTTGGGGAGCTGGAGGCCCTTAAACACATGCATAACCCCACCAAATCTGTAAGTCTTTTTGTAACCTGACCCCCTCCAGGGCGGAAGTGTGGGCAACAATGAATGAATTTGAAAATTGGAATCAAACTGGGCCTGTAGAGATTTTCTTGTGTGCTTGCTCTATGCAAAACAGAAAGAAAGAGAGTGCAGAGGTCTTAGCTGAGGTCGGCGTCTAGGCTGAGTGTGTCCAGGTTCTTTGGCTCTTATGCAAAGACTTGATCTAAAACCATCCAAAGATTTGCAGAAACAGTAGGGGGACTTGACTCAAAGCAAAGAGACAGAAAAGGTCAGGTACAGTAAGAGAGACTGGGCCACATGAGTGAGGGTACTCAGGGACCCCAGTTATTGTTTGGGGTTTGTTTTTACAGCGTTCAAGAGAAGAGGAGTGTTAGTTTGGGTGGTTCTTTAAGTGACAGACTGAATTATATAACCATCTTTCTGTCATGAATGCCCCTTCCCATAACACGTCTGATTTTGATCGCAAATGCACCTAATTTTGTATAGGAATAAGAAGCTCGACCTACTACACAAACCTAGCCCAGGAGCTTCCTACTTTCTTATACAGACACAAGGAGAACATCATTGGATAGAATCTATCTATGTTGGATGGTTGTTAAGGAAAGGAGACAGTTCCACTGTTCAGAGTGGAATGTGTGTACAGCTCAGTGCAGATGGGGGCCCTAGGTTGCTAATAAATTGCTAGGTACACGTGCAGAAAGGCATATGTGTGCATAGTACAGTATAAAGTTCCTAGGCTGCCAAATGCTCCATTGGAAGAGGTGAGGGTACATAGTTCAAATCAAGAGGAGTCCCAGGTTGGTAAGCTATTCCCTATGCTTGCTTGTCTCTAATGTGTCACAGAAGCTTGGGTTTCAGATCTCAGATGACTACCGGCTCTTGGAACTGGTTCTTTCCATTGTTCCCTATTTCCCTTACTGTCCTTTGTCCTTATCCACACACTGAAACCAAGTTGGCATCCTGAGAAATGGCTAGAATTGATCCCTTTAAAAATAGCTGTGATATGCTCACTCCTAGGAGGGAAGAGCTGAGCCCTCTTCTCTTTTCCATCCCTCCCCATTCCTCACCAG
Seq C2 exon
CTCTTCAGCGATGTGGCTTATAAAGCACGGAATCGAGAAGATCTGATCGCAGGAGTTGATGAATTTCTAGATGAGGTCATTGTCCTTCCCCCTGGAGAGTGGGATCCAAACATCAGAATTGAGCCGCCCAAGAAAGTTCCCTCAGCCGACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010378:ENSRNOT00000014249:10
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=0.154
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(10.8=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(13.4=69.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTTCATACTTCTAGGACCTTCTGG
R:
TCTTGTCGGCTGAGGGAACTT
Band lengths:
238-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]