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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattctttgttccag

Basic information

species Arabidopsis thaliana
transcript AT5G51820.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA20G29230.1 (Glycine max), 5'ss of exon 20
GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattctttgttccag--
|| ||||||||||| | ||| || ||||||||||||||||| || || ||||| || || || |||| ||||||||| |||||| | |  |  ||  || |   | ||   |   |   |    ||  ||  ||   |  | ||   | | ||  |   | |   |     |  ||  || ||  |   
GTAGATGGAAGTGTGGTATCAAAACAAGGTGTTCGGTTTGTTTTTACAGATGGTTCAAGGATTATATATCGTTTATCAgtatgtggaatctgtttgtttgtccaccttgtccctttcaaagaagttgaatccatcttggaa-atctacgcataaaatt-taagtcagtgctgtttttatttttttacag

upper sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 20
GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta---gattcttt------ctttttttctttaatcaaattccat--gttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattctttgttccag---
|| ||||||||||| | ||| || ||||||||||||||||| || || || || || || || |||| ||||||||| |||||| | |   | || |||      ||| |    || ||  || ||  ||   | ||  |  | |||    | | |       ||  |  |    |  |||    || ||  ||       
GTAGATGGAAGTGTGGTATCAAAACAAGGTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacag

upper sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 5'ss of exon 20
GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaact--tagaattctttgttccag
|| ||||||||||| ||||| |||||||||||||| ||||| || ||||||||||| || ||||||| ||||||||| ||| |      ||  ||  |     | ||||      ||| ||   |  |       | ||  ||||  |  || |      ||| |||||  | |   || |  || |||
GTGGATGGAAGTGTGGCATCAAAGCAAGGTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCAgtaggc-----atcattaatcaacctatttatatctcttctattcctctt------ggggatccatttacaactgtggtg--gaagtaactattgggtctcatatttacag

Mapped 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|125293991|gb|EL308076.1|EL308076
EST:     GGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTAGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGA
genomic: GGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACT-GGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGA
EST: gi|125255042|gb|EL269127.1|EL269127
EST:     TTCACGGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
genomic: TTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
EST: gi|86088359|gb|DR384118.1|DR384118
EST:     GTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
genomic: GTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattctttgttccag

- - - - - - - - - - - - - - - - - - - - - - - - GATGGA