RnoINT0138377 @ rn6
Intron Retention
Gene
ENSRNOG00000020951 | Slc4a1
Description
solute carrier family 4 member 1 [Source:RGD Symbol;Acc:3710]
Coordinates
chr10:90301807-90303464:-
Coord C1 exon
chr10:90303270-90303464
Coord A exon
chr10:90301978-90303269
Coord C2 exon
chr10:90301807-90301977
Length
1292 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
3' ss Seq
CAGTGTTTTGTCGGTTACAGATT
3' ss Score
8.26
Exon sequences
Seq C1 exon
TTCTGTGAAAGCAATAACCTGGAGTACATCGTGGGCCGCGCGTGGATCGGCTTCTGGCTTATCCTGCTGGTGGTGTTGGTGGTGGCCTTTGAAGGCAGCTTCCTGGTCCAATACATCTCCCGCTACACTCAGGAGATCTTCTCCTTCCTCATCTCCCTCATCTTCATCTATGAGACTTTCTCTAAGCTGATCAAG
Seq A exon
GTGGGGCCAGAGAGGATGCTAACACTCATGCATCATCGCATGTCTGCGAGAGTGTGCTACGTGTCTGTAGAGCGTGACTGTGGCCATGTTTCCACCACCTGTGTGCGCGGTTCTGAATGTGGGCACACGTATGTGTTGGCGTTCATCTAGGATTCTGCAGTTGGGTTTCTTGGGACCGCTTGAGACTCAGTGCTCATGTCCTGACTGTATAAGGGAGGTCACCTCTATCTACGCTTTTTCATATTTATGACCACACATCACGTGACTAGTGGGCACTCTCTGTGGGATGGCCAGGAAGTCATGCGCAGAGAGGGAGGAGATGCTTGGAAGCCCTGGGCCTTTTCTTTCTTTCTTTTTACTTTATGTGAGCACACTGTCACTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCACTCCAGCCCCCAACCCTAGGTCTTTCCTTTTCTGCATTTCCCCTCCAGAACCCCATAGGGCCTCTGCCTCCATAGCTTGCCTCCTCCCCCCAAGAGCTCCTCCCACCTCCACATCTGCACTGTGTATGAAAGAAGGGTGACCTGTGCGTGTCCTGACTCTGTTGACTGACGGGCTCTTTTATCTTCTGTAGATCTTTTTTTTTTTTCTTTTTTTTGGAGCTGGGCACCGAACCCAGGGCCTTGGGCTTGCTAGGCAAGCACTCTACCACTGAGCTAAATCCCCAACCCTTCTGTAGATCTTTTAAGGAGATTTTACTTATTTCCTTATTTATTGTGCTGGGGTTCAAGCTTCTTGCATGCTGGGTAAATGCTGTCCCTGTCACCAACTCCTTAAGCCCTTTTTATAAACCTTATTACTTACTGCTGTCTCCAGAATTCTCACCTTCCACACAACGTCTGGAAGCATATACCTGCGCGTGCAGTCTCACTGCCTCTCGGACACTTCCCACACGAGCTAACTTGATCTTGGTCCTAAAAACAAACAAACAAACAAACAAACAAACAAACAAGCCAAGCAGGTTAATAAGTCAGATGAGAAAGAAGGTGGACTGGACGGGTGATGGTGATGGTTGTATGGGCAGTAGATGGGTAGATGGATGTTTGGGAGTACGTATGGATAGATGGATGTACAAACAGCAGGTTGATAGTGCCCAGTCAACTTCTCTGATGCTGTCTAGCTCAAGCCGAGGCTTGGGAGGGAACACAGTGTTTTGTCGGTTACAG
Seq C2 exon
ATTTTCCAGGACTACCCGCTACAAGAGAGCTATGCCCCTGTTGTGATGAAGCCCAAACCTCAGGGCCCCGTGCCCAACACAGCCCTCCTCTCCCTTGTGCTTATGGTTGGTACCTTCCTACTTGCCATGATGCTACGAAAGTTCAAGAACAGCACCTACTTCCCCGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020951:ENSRNOT00000028445:13
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=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=FE(33.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=PD(9.9=33.3),PF0095516=HCO3_cotransp=PU(15.8=78.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCTGGAGTACATCGTGGGC
R:
CGGGGAAGTAGGTGCTGTTCT
Band lengths:
346-1638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]