Sequence
atgc intronic sequence ATGC exonic sequenceGCGTCGTGGCAGTGGGAAAATGCCACCGCCGGCGCCGTCGCTGGATTCGCCACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGgtctggtttttcactcctggattaactcatcgattttgcttttaaaaagttgctaacttgattgaacaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66380.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66380.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G05890.1 (Glycine max), 5'ss of exon 1
GCGTCGTGGCAGTGGGAAAATGCCACCGCCGGCGCCGTCGCTGGATTCGCCACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGgtctggtttttcactcctggattaactcatcgattttgcttttaaaaagttgctaacttgattgaacaacag------------
| ||||||||||| || |||||||||||||||| |||||||||||||||||| || | ||||| | || |||||||| || || || ||||||||| | | | | || || ||| || | || | |||| | | | || | | || |
GACCAATGGCAGTGGGAGAACGCCACCGCCGGCGCCGCCGCTGGATTCGCCACCGTCGCCGTCATGCATCCCCTCGATGTTGTCCGAACTAGGTTCCAAGgttttctctcgctcttctcatataaaccaacatttcttatttttcacgccttcgaattcttagaagcattatttgattctgcag
upper sequence: AT5G66380.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA16G24580.2 (Glycine max), 5'ss of exon 1
GCGTCGTGGCAGTGGGAAAATGCCACCGCCGGCGCCGTCGCTGGATTCGCCACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGgtctggttt--ttcactc--ctggattaactcatcgattttgcttttaaaaagttgctaacttgattgaacaacag------------
| ||||||||||| || |||||||||||||||| ||| ||||||||||| || || | ||||| | || |||||||| || || || ||||||||| | | |||||| || ||| || | || | |||| | | | || | | || |
GACCAATGGCAGTGGGAGAACGCCACCGCCGGCGCCGCCGCCGGATTCGCCACTGTCGCCGTCATGCATCCCCTCGATGTTGTCCGAACTAGGTTCCAAGgttctctctcactcactcttctcatataaaccaacatttcttatttttgacgccttcgaattcttagaagcattatttgtttctgcag
upper sequence: AT5G66380.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv04s0023g02600.t01 (Vitis vinifera), 5'ss of exon 1
---------------GCGTCGTGGCAGTGGGAAAATGCCACCGCCGGCGCCGTCGCTGGATTCGCCACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGg--tctggtttttcactcctggattaactcatcga---ttttgcttttaaaaagttgctaacttgattgaacaacag------------------------------------
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TCGGCGTTGGATAGAAGGAAGTGGGAATGGGAGAATGCCACCGCCGGCGCCATCGCCGGATTTGCGACCGTCGCTGCTATGCACCCTCTGGATGTCGTCCgtactagatttgcaggcatccatttgtctttttatatattgactctctttatcttttacattttccttttcgatatggagat-gcataatggtcgatgttcatattggctttgaattgatttgaacagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|152037821|gb|BP799055.2|BP799055EST: CACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAG TCAACGACGGAAGAGGGTCAAGTCTGCCGACGTACAAGAACACTGCTCACG
genomic: CACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGgtctggtttt ... tgaacaacagTCAACGACGGAAGAGGGTCAAGTCTGCCGACGTACAAGAACACTGCTCACG
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCGTCGTGGCAGTGGGAAAATGCCACCGCCGGCGCCGTCGCTGGATTCGCCACCGTAGCTGCTATGCACTCTCTTGATGTTGTTCGTACGAGATTCCAAGgtctggtttttcactcctggattaactcatcgattttgcttttaaaaagttgctaacttgattgaacaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT