DreINT0150760 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20505936-20507792:+
Coord C1 exon
chr23:20505936-20506086
Coord A exon
chr23:20506087-20507728
Coord C2 exon
chr23:20507729-20507792
Length
1642 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GGTTTGTCTGTGTCCCTCAGCCC
3' ss Score
6.12
Exon sequences
Seq C1 exon
GACTTCCACTTTCCTCTTTTTATGACCCTGGTCCATCTCACTATAATATTCTGTTTATCCACACTGACACGCTCTGCTATGCAGTGCTGGACAGGAAAGCCTCGAGTTACTCTTCCCTGGAAGGTCTACCTTTCTAAAGTAGCCCCTACAG
Seq A exon
GTGAGAATTAAAGTCATCATGAGTCCAAAGACCAAACAAAGTGTTTGAATAGATTAAACCCGTTATCTTTTTTTATCCAACACACAGTTTGGGCAGGTAAAGTCCACATCAGGGCCATTCACACTGTGCTTAATCTGGATTATTGTTGTTCTGTACACCACTTTTAACTATGTATAAACCCAACAAACGCACAACGTTGCCTCAACGTAGCTTCCTTCCTACATCGTTGTACCAATACTGTAAAAAGGTTGAGGATCTACGTTGTTGCTGATGGTTGACACAACAGTGTCATAATGTTGCCATTTAATGGCTGTTGCTTTAGGTTGTAGACAACCACTGTACAACATTTACCCGTTATAAATGAATCGGTTTAAATTTCGACAGACCATTCTGTGTCTCATTCAACAACGTTCACTGCATATTGTGACTTGTGGCTACTGTGGATCCATCTGTGAATTGAATTCTCTGTTGGATTTGTTTCTTTCTCTGACTACTTTCTCCGCACCTACAGCTATGCCTGGTTTTCGGCTGCGCTCCCCGATCTGTTGTATTCTCCAGTTTAGTTTAATTATACAGTTGAAGTCAGAATTATTAGCCTCCATGTTTATTTTTTCCCCCAATTTCTGTTTAACGAAAGAAGATTTTTTCAACACATTTCTAAATATAAAAGTTTTAAATACTCATTTCTATTAACTCATTTATTTTCTCTTTGCCATGATGACAGTAAATAATTTTTTACTATGTATTTTTCAAGACACGTCTGTACAGCTTAAATTGACATTTAAAGGCTTAACAAGGTTAACTAGGCAGGTTAGGGTAATTAGGCAAGTTATTGTTTAACGATGGTTTGTTCTGTAGACTTTTGAAAAAATATATAGCTTAAAGGGGCTAATAATTTTGACCTTAAAATGGTTTTTAAAAAAATTAATAACTGTTTTTATTCTAGCTTAAATAAAACAAATAAGACTTTCTCCAGATGAGTAAATATTATCAGACAGACTGTGAAAATTTCCTTGCTTTGTTAAACATCATTTGGGAAAAAAAATAAAATAAAAATCAAAGGGGGGCTAATAATTCTGACCTCAGCTGTATATAGTTAGTTAATTATTTAATGTAATCTATATGCATTTGTGTGGCATTTTTACATGTAAAAAATTATATATGCACTCAGGCCTATATTAAAAAGGAAAAAATGAATGAGCAATATTTAATATTAAAAGCAATACTGGAAAACCATTTCTGCTTATCCTGTATTCTAGACGGTATTGATTAACTGCCAGGAAAAAACAATAAATACATGTACTAAGAACGTCGTCTCACGGTTGCTGAATGTTACACGACAACATTGCTACAACCTTTTTAGTCGTTTTACATTTCTACGTTGTGACCATGTAGCGAGCATGTAAGTGGAGACGTTGGCTTTGACAAAATTCAGCGTTGTACGGATATCGTTGCAATGTAGTTGAATTTGTTGGGAATAAACATTTAATGTGATTTAGAAGCACAGTGGGTACTGCAGTGTCATCTATTCATGATCAGTTAATGTTCAAAAAGTAACACAGAATGATATAAACCTTGCATTCTAGTGTGAAAATGGTTGATCATAATAATATCTGTTCATCGGTTTGTCTGTGTCCCTCAG
Seq C2 exon
CCCTGGCGACAACGTTGGATATTGGACTGTCCAACTGGAGTTTCCTTTTCATCACTATTAGTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:3
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:
PF0089215=EamA=FE(36.0=100)
A:
NA
C2:
PF0089215=EamA=FE(15.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTCCACTTTCCTCTTTTTATGACC
R:
AGTGATGAAAAGGAAACTCCAGT
Band lengths:
206-1848
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]