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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAGGGTTTGATGGTGCAGATCCGATCGATCCAAACTCCATACTGGTTGAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagcttttttttgctacaaaagcttacatattgttttgaaactttttaaaaactattagttggattttggtttgaag

Basic information

species Arabidopsis thaliana
transcript AT5G18170.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G04560.2 (Glycine max), 5'ss of exon 7
TCAAAGGGTTTGATGGTGCAGATCCGATCGATCCAAACTCCATACTGGTTGAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctttt-ttttgctacaaaag-cttacatattgttttgaaactttttaaaaactattagttggattt--tggtttgaag---------------
| ||||| ||  |||||   ||||| || || || ||||| ||| ||||||| ||||||||| | || ||||| ||||| ||||| ||||||||||| |||| |      |  |||  ||||||||  |||   |  |    | |  |   | |   ||   |      ||||  |  ||| ||                
TAAAAGGATTCAATGGTAGTGATCCAATAGACCCTAACTCAATATTGGTTGAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcctaatttaactacaaaattcttttgttctcaactcaggcaaataagggacacctcaaaatatttgattattttaacaaactacatgatggc

upper sequence: AT5G18170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 5'ss of exon 8
TCAAAGGGTTTGATGGTGCAGATCCGATCGATCCAAACTCCATACTGGTTGAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttag-------agcttttttttgctacaaaagcttacatattgttttgaaactttttaaaaactattagttggattttggtttgaag---------------
||||||| ||  |||| |||||||| || |||||||| || ||| ||||||| ||||||||  ||||| |||| ||||| ||||| ||||| |||||||||||         ||| | | |||  |    ||| | || | || || |    |||| | | || | ||| |   |||  |   | ||                
TCAAAGGTTTCAATGGGGCAGATCCAATAGATCCAAAGTCAATATTGGTTGAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAGgttcttctcaccagcatctgttt--tgttgaagttcac-tgttcttcttgttctttgttataatttttattgctattcagaaattaatagatctttatcttaa
















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|116445683|gb|EG488275.1|EG488275
EST:     GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGCCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
genomic: GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
EST: gi|164000797|gb|EL971803.1|EL971803
EST:     CTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
genomic: CTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
EST: gi|86055070|gb|DR350827.1|DR350827
EST:     TCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
genomic: TCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
EST: gi|116445672|gb|EG488264.1|EG488264
EST:     AGGATTGTGATATCCTCGTCCCCTGCAGCACTTGGTGGTGCCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
genomic: AGGATTGTGATATCCTCGT-CCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
EST: gi|164033567|gb|ES040851.1|ES040851
EST:     GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCAT
genomic: GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCAT
EST: gi|116386886|gb|EG429478.1|EG429478
EST:     GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAG                         GGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA
genomic: GAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagctt ... tggtttgaagGGAGAATGCGAATGAGATTAAAGCAAAGTTCATCATAGAAGCAGCTAATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAGGGTTTGATGGTGCAGATCCGATCGATCCAAACTCCATACTGGTTGAGGATTGTGATATCCTCGTCCCTGCAGCACTTGGTGGTGTCATCAACAGgttagagcttttttttgctacaaaagcttacatattgttttgaaactttttaaaaactattagttggattttggtttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG