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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatccttttaatcatgagtgactttttttttagctccattcattgtttacattgatttttaaatgtttctgtaatttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G54080.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 7
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatccttttaatcatgagtgactttttttttagctccattcattgtt--tacattgatttttaaatgtttctgtaatttgcag----
 || || || ||||||||||| |||||||||||||| || ||||| |||||||||||||| ||| | |||||||||||    | || || | |   |   | | ||||| ||||  |  | |  || ||  | |  || |  || |   | | ||| |||    |    
AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAGgta--gtgtcattgtgacagt---ttaatttttatttatttgtacttttttttggtgcggtgctgattgatcatctttgttattcattgacag

upper sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM5G835213_T01 (Zea mays), 5'ss of exon 8
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttat----atccttttaatcatgagtgactttttttttagctccattcattgtttacattgatttttaaatgtttctgtaatttg-cag
 || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||||  | |    ||  ||| || | |  |||  || ||     |  |  ||     |     || || |    ||||   | |   ||  |||
AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgccattatttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacag

upper sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttat----atccttttaatcatgagtgacttttttt--ttagctcc---attcattgtttacattgatttttaaatgtttctgtaatttgcag----
 || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||||  | |    ||  ||| || | |  |||  || ||    | | ||     |     |||||    |  || |   ||  |||  |||   |  |    
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca

upper sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 8
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttat----atccttttaatcatgagtgactttttttttagctccattcattgtttacattgatttttaaatgtttctgtaatttg-cag
 || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||||  | |    ||  ||| || | |  |||  || ||     |  |  ||     |     || || |    ||||   | |   ||  |||
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacag

upper sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 7
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatccttttaatcatgagtgactttttttttagctccattcattgtttacattgatttttaaatgtttctgtaattt--gcag
 || || || || |||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||||||||| |||||   |  |   ||| || ||   | | ||||  | |  |     || || ||    ||     ||| || |||||  |||||  | ||
AGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAGgtccaaatttggttttataatct-taatttttggtgtgacaaggctctttattatggttttgacttagatttttcttgaatttttgtag

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|124936299|gb|EL013215.1|EL013215
EST:     TTTCCTTCCGTAATCAGCAG                         GATGCTCAAACTGCCATAAATGAGATGAATG
genomic: TTTCCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGATGAATG
EST: gi|86052517|gb|DR348274.1|DR348274
EST:     CTGGACGCTCAAGAAGGNNTTTTGGTTTTGTTTCCTTCCGGAATCAGCAG                         GATGCTCAAACTGCCATTAATGGAGATGAATGGTAAATGGG
genomic: CTGGACGCTCAAGA-GGC-TTT-GGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATG-AGATGAATGGTAAATGGG
EST: gi|86052513|gb|DR348270.1|DR348270
EST:     AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG                         GATGCTCAAACTGCCATTAATGAGATGAATG
genomic: AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGATGAATG
EST: gi|125247911|gb|EL261996.1|EL261996
EST:     TTCCGTAATCAGCAG                         GATGCTCAAACTGCCATAAATGAGATGAATG
genomic: TTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGATGAATG
EST: gi|124846534|gb|EH930971.1|EH930971
EST:     AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG                         GATGCTCAAACTGCCATAAATGAGA
genomic: AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGA
EST: gi|125030133|gb|EL102402.1|EL102402
EST:     CCTTCCGTAATCAGCAG                         GATGCTCAAACTGCCATAAATGAGATGAATG
genomic: CCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGATGAATG
EST: gi|86052514|gb|DR348271.1|DR348271
EST:     AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG                         GATGCTCAAACTGCCATTAATGAGATGAATG
genomic: AAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatc ... taatttgcagGATGCTCAAACTGCCATAAATGAGATGAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttatatccttttaatcatgagtgactttttttttagctccattcattgtttacattgatttttaaatgtttctgtaatttgcag

- - - - - - - - - - - - - - - - - - -  AAGAGG