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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcag

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA09G40150.1 (Glycine max), 5'ss of exon 7
GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttt--tttttgatgagt--tcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcag
||||||||||| |||||||| |||||| |||| |||||||| || ||||||||||||||| ||| |||||  |||||  | |    | |   || ||    ||  ||||            | | |   || | |    ||
GTTAATCCCCAGACTCATCAGTTAAAAGTATGTGATTTTGGGAGTGCAAAGATGTTGgtaagtttattttcgtttttccttatcaatttgaaagttgtacaatagtttgtgcctgagcttgtgatattatt-gtgctatag

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G45960.1 (Glycine max), 5'ss of exon 7
GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttttt---tttgatgagttcttggaga--tgagttatcatttgaataatgatggctaacaccctttgcgtctcag-
 |||||||||| |||||||| |||||| |||| |||||||| || ||||||||||||||| |||  ||||||   |||  |     ||| || |  ||    |   ||||  |         | | |   || | |  | || 
-TTAATCCCCAGACTCATCAGTTAAAAGTATGTGATTTTGGGAGTGCAAAGATGTTGGtaagtttgttttttgtttttccttgtcactttgaaagttgtacaacagtttgtgtctgagcttgtgatattatt-gtgctttagg

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcag---
|| |||||||| ||||||||  |||| ||||| |||||||| || ||||||| ||||||||||| ||| | ||     || || ||  | |  | ||  |  | | |    | |    |||  | ||||| |    |   
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatcttccttggaatttttcaacactaatttgctatagca----ggttttgaacttcatttgcctgatggtag

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|164172042|gb|ES040079.1|ES040079
EST:     ATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACACGGCC
genomic: ATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
EST: gi|124857013|gb|EH941450.1|EH941450
EST:     TCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTA
genomic: TCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTA
EST: gi|125116831|gb|EL166214.1|EL166214
EST:     CCAAACTCATCAATTAAAAATATGCGATTTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATAT
genomic: CCAAACTCATCAATTAAAAATATGCGATTTT-GGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATAT
EST: gi|125244903|gb|EL258988.1|EL258988
EST:     CCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATAT
genomic: CCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATAT
EST: gi|124787604|gb|EH877283.1|EH877283
EST:     GGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
genomic: GGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
EST: gi|164032470|gb|ES068755.1|ES068755
EST:     ATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
genomic: ATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcag

- - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGATG