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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G60750.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcaca---gaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
||||| || |||||||| ||| | ||||||||||||||||| ||||| ||||| ||||| |||||||| || ||| ||||||| || |||||| ||  || |    |      ||| || |  | | | |  ||  |     |||   ||  | ||||| || |     | |  | | || |||    | | || ||
GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatctcaactga---agctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggttt---cgttctgtag

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
||||| || |||||||||||| | |||||||||||||  ||||| || || |||||||| || |||||||| ||| ||||||| || || ||| ||   |||    ||| ||||  | ||  | |   |              || | || |||||     | | ||  | | ||   | ||| |||| |||||
GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgt--tttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgag---aaagtttgggtttcctatatggttgctgtgcag

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA03G03200.1 (Glycine max), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgc-tctctgctttggctgctatgcag
|| || ||||||| | | || || |||||||| ||||  || || ||||| ||||||||||| |||||||| ||||||||||| || || ||||||| ||         ||||  | || |   | || |   ||   |     ||| | ||  ||| | |  | || | | |   |||| |   ||        
GAAGAGGATTTGAGGGAATTTCGCCAATGGGGGAGCAGAACTCCGGGACACCCTGAGAATTTTGAGACTCCGGGAATTGAAGTTACAACAGgtttgatatgagttagagtttgtataatagaata-gtaattctttttattttttattttta-ttgtttatttatttatccattattgctatttttgtag-----

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G38720.1 (Glycine max), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
|| |||||  ||||| | ||||| |||||||| |||| ||| || |||||||||||||| || |||||   |||||||||||| ||||| |||| || ||||        || | |||||  | || ||  ||   |  ||  || | |     |||  |     || | |||  || ||||  |         
GAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatttca------ttagtttatg--ttat-tgttatcatagtgagcctttttgctg-tgtcctgttgcttatcctcg-tgttttgtttag-------

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggt-tcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
||  ||||  | ||| | ||||| |||||||||||||  || || |||||||||||||| || ||||| | |||| ||||||| || || |||| ||  |||   |  |||  | |  || | |||||   |   |    |      ||| |  || |||   ||      |  | || || |            
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgct-tatcctca------cgttttgtttag------------

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggctta---tggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
|| ||||| |||||    |||||||||||||||||||  ||||| || || || || ||||| ||||| |||||  ||||||||||||||||||  ||||| |  |  |    | | |   || ||  | ||      || | ||   |    |   |||   |           ||   |||||  |         
GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgtt--agattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtag-------

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ07729 (Selaginella moellendorffii), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgt--ttgagattttgcttcttttggcttatggttcat-gtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
|| || ||||||||||| |||||||||||| | ||||  || || || ||||| ||||| ||||||||||| ||  | |||||||| ||||||  |||     |  ||  | |||  |  | ||| || |||   |       ||||                                                  
GAAGAGGATTTGAAGCAATTCCGTCAATGGAGCAGCAGAACTCCTGGTCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTGgtaattgttgactcactcgtgttgaatggttgttgattgtggcttgcttttcaaacag------------------------------------------------

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ07676 (Selaginella moellendorffii), 5'ss of exon 2
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgt--ttgagattttgcttcttttggcttatggttcat-gtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag
|| || ||||||||||| |||||||||||||| ||||  || || || ||||| ||||| ||||||||||| ||  | |||||||| ||||||  |||     |  ||  | |||  |  | ||| || |||   |       ||||                                                  
GAAGAGGATTTGAAGCAATTCCGTCAATGGGGCAGCAGAACTCCTGGCCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTGgtaattgttgactcactcgtgttgaatggttgttgattgtggcttgcttttcaaacag------------------------------------------------

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|86072919|gb|DR368676.1|DR368676
EST:     AAGTCACTACTG                         GTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGA
genomic: AAGTCACTACTGgtttgagatt ... tgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGA
EST: gi|125303775|gb|EL317860.1|EL317860
EST:     ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG                         GTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCT
genomic: ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagatt ... tgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCT
EST: gi|124839040|gb|EH923479.1|EH923479
EST:     ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG                         GTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTA
genomic: ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagatt ... tgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTA
EST: gi|125202075|gb|EL217029.1|EL217029
EST:     ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG                         GTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGA
genomic: ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagatt ... tgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGA
EST: gi|125293607|gb|EL307692.1|EL307692
EST:     ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG                         GTCCTCTTGGACAAGG
genomic: ACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagatt ... tgctatgcagGTCCTCTTGGACAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG