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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatcgataacacaagaactcatccctgaaactccgaaaataaaaatcctaatctgtttggttttggcag

Basic information

species Arabidopsis thaliana
transcript AT5G07440.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatcgataacacaagaactcatccctgaaactccgaaaataaaaatcctaatctgtttggttttggcag---------------------------
|||||||||    ||||||||||| || |||||| | || || ||||| |||||||| |||||||| ||||| |||||||       | || |||      | |  ||    ||  || ||  | |     ||| |      |||||||||                           
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaa--acatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag

upper sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA01G41310.1 (Glycine max), 5'ss of exon 7
GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaa------tgcatcgataac--acaagaactcatccctgaaactccgaaaataaaaatcctaatctgtttggttttggcag------
|||||||||||  |||||||| || || |||||| |||| || || || |||||||| || || ||||||||||||||||      ||| | | |      || ||  | |    ||       || | || | |   ||||     || |||            
GGAAAATGCTGCTGATGTGAAAGCGAAATTTATAATAGAAGCTGCAAATCATCCAACTGACCCTGATGCTGATGAGgtaaggttattgctttgttgttttgcatgagatgagatatgctgaattgatattagagaatataatggaagtgatttcatttattgtag

upper sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G15740.1 (Glycine max), 5'ss of exon 8
GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaa-tgcatcgat----aacacaagaactcatccctgaa-----actccgaaaataaaaatcctaatctgtttggtt---ttggcag
|||||||||||  |||||||||||||| |||||| |||| ||||| || || || || || || ||||| |||| ||||| |  |  ||       |      | |  |     ||     |  | |||  || |   | ||||      | ||   || ||||
GGAAAATGCTGCTGATGTGAAGGCAAAATTTATAATAGAAGCAGCAAATCACCCCACTGACCCTGATGCGGATGGGgtaagtttactgacttgcggctatgccatttgttgtgaaatatatatcctgaacttacattacataatgaaagcgattctttttgcag

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|116402756|gb|EG445348.1|EG445348
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAT                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|116403318|gb|EG445910.1|EG445910
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|116401898|gb|EG444490.1|EG444490
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|116401662|gb|EG444254.1|EG444254
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|301502280|gb|HO207820.1|HO207820
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|164218092|gb|ES123640.1|ES123640
EST:     GTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCT
genomic: GTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCT
EST: gi|116400111|gb|EG442703.1|EG442703
EST:     GGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
EST: gi|116402354|gb|EG444946.1|EG444946
EST:     AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAG                         ATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA
genomic: AGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatc ... gttttggcagATTCTGTCGAAGAAAGGAGTGATTATACTTCCAGATATCTACGCAAACGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatcgataacacaagaactcatccctgaaactccgaaaataaaaatcctaatctgtttggttttggcag

- - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT