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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaaatgactaaatgcagtcaacaataatactcaagaatttataaatgttcaatcattgttggtgtcttcttgcttttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG

Basic information

species Glycine max
transcript GLYMA07G06230.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 7
tagaaatgactaaatgcagtcaacaa--taatactcaagaatttataaatgttcaatcattgttggtgtcttcttgcttttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG
     | |  | ||||   ||       |  || |   |  | |  || ||| || |  || |      ||  ||  |   |      |  ||   |||||||| |||||||  | ||||||||||| || || |||||| | |||||||||||||| ||||| || || |||||||| ||| |||| ||||
---gtaagtttcaatgtcatccttctctttttatttctggctatggaattgt-cagtt-ttataaagagctgatta-tcagataaagatatgtatgttgcagATTTAGGAGCCTTAGGAAACTATCCAGGCTCTCCATTTCTTCCATCTGATTCAGAGATTTTCCTGGATTCTCCTGAACAAGAGGACATAG

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 7
lower sequence: AT2G46420.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------tagaaatgactaaatgcagtcaacaataatactcaagaatttataaatgttcaatcattgttggtgtcttcttgctt-ttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG
                                 |  ||  |   | |  | || |    |    |  |  |  |||| ||    |  |   |    | |||| | | | ||   |   | |||||||||| |||| ||| | ||||||||||| ||||| || ||| |||||||||||||||| ||||| || || ||||| || ||| |||| ||||
gtaagctctttttatcaaatgccattgcgagtttagctcgaaaaactttataacatacgttggtagatgctccatgtacaggtgtactccatagaatgttgcatatcaatgatcttt-tactttgcagATTTAGGGGCTTTAGGAAACTATCCCGGTTCTCCTTTTCTGCCATCTGATTCAGAGATTTTACTTGACTCTCCCGAACAAGAGGACATAG

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 7
lower sequence: AT2G46420.2 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------tagaaatgactaaatgcagtcaacaataatactcaagaatttataaatgttcaatcattgttggtgtcttcttgctt-ttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG----------
                                 |  ||  |   | |  | || |    |    |  |  |  |||| ||    |  |   |    | |||| | | | ||   |   | |||||||||| |||| ||| | ||||||||||| ||||| || ||| |||||||||||||||| ||||| || || ||||| || ||| |||| ||||          
gtaagctctttttatcaaatgccattgcgagtttagctcgaaaaactttataacatacgttggtagatgctccatgtacaggtgtactccatagaatgttgcatatcaatgatcttt-tactttgcagATTTAGGGGCTTTAGGAAACTATCCCGGTTCTCCTTTTCTGCCATCTGATTCAGAGATTTTACTTGACTCTCCCGAACAAGAGGACATAGGTAAACATTA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G61700.2 (Arabidopsis thaliana), 3'ss of exon 7
tagaaatgactaaatgcagtcaacaa--taatactcaagaatttataaatgttcaatcattgttggtgtcttcttgcttttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG
     | |  | ||||   ||       |  || |   |  | |  || ||| || |  || |      ||  ||  |   |      |  ||   |||||||| |||||||  | ||||||||||| || || |||||| | |||||||||||||| ||||| || || |||||||| ||| ||||     
---gtaagtttcaatgtcatccttctctttttatttctggctatggaattgt-cagtt-ttataaagagctgatta-tcagataaagATATGTATGTTGCAGATTTAGGAGCCTTAGGAAACTATCCAGGCTCTCCATTTCTTCCATCTGATTCAGAGATTTTCCTGGATTCTCCTGAACAAGAGGA-----

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 7
tagaaatgactaaatgcagtcaacaataatactcaagaatttataaatgttcaatc-attgttggtgtcttcttgcttttactgtct----tgagttc-tttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG
      |||  |  |  |    | |  | | ||   | ||  || | | |  |||| ||| |  |   | || || ||| |   | |    |||  || |||||||||||||||||| |||||||||| || ||||| || ||| ||   |||||||||||||||||||| || ||||| || ||| |||||||||
------tgagaaggtatatggtatatcactgctgctgcatggattattttgtaatccattatgagcaacctcatgttttgataatttgtggtgaaatcgtttgcagATCTAGGAGCTTTGGGAAACTACCCCGGTTCTCCCTTTCTGGGTTCTGATTCAGACATTTTGCTTGATTCTCCGGAGCAAGAGGATATAG

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|17401879|gb|BM178661.1|BM178661
EST:     ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAG                         ATCTAGGAGCTCTGGGA
genomic: ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAGgtgatttctt ... ttctttgcagATCTAGGAGCTCTGGGA
EST: gi|120497096|gb|EH225263.1|EH225263
EST:     ATGGAATNTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAG                         ATCTAGGAGCTCTGGGAAACTATCCT
genomic: ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAGgtgatttctt ... ttctttgcagATCTAGGAGCTCTGGGAAACTATCCT
EST: gi|193604438|gb|FK555889.1|FK555889
EST:     ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAG                         ATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT
genomic: ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAGgtgatttctt ... ttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT
EST: gi|12689880|gb|BG156216.1|BG156216
EST:     GGCAGATTTGCCAAACTTGGGAG                         ATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT
genomic: GGCAGATTTGCCAAACTTGGGAGgtgatttctt ... ttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT
EST: gi|6913615|gb|AW395145.1|AW395145
EST:     ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAG                         ATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT
genomic: ATGGAATTTTAGCCTATCTGATCTAACGGCAGATTTGCCAAACTTGGGAGgtgatttctt ... ttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttcaatcattgttggtgtcttcttgcttttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG
                                             ttctttgc  CT-rich tract
       aatcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaaatgactaaatgcagtcaacaataatactcaagaatttataaatgttcaatcattgttggtgtcttcttgcttttactgtcttgagttctttgcagATCTAGGAGCTCTGGGAAACTATCCTGGTTCACCATTTTTGCCATCTGATTCAGACATTTTGCTAGAATCTCCTGATCAACAGGATATAG

- - - - - - - tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtg