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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaggaaagtaaggtattgtgtgatttactcattttaaatccctattaatttcttgttcattgattatttatttcttcttttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

Basic information

species Glycine max
transcript GLYMA12G28730.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
---gaaggaaagtaaggtattgtgtgatttactcattttaaatccctattaatttcttgttcattgattatttatttc--ttcttttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
          ||| |   | | | |   |  || |  ||   |   | | |  | |    ||   ||||  |  |||   ||  ||| ||| ||||   |||||||| ||| | || |||||||||||||||||||||||||| || || || ||||| |||||||| |||||  | |||
caatcgttggagtcaaacaatttctagctgccttacctt---ttagtgtca--tacccaatcgcagatttctgctttgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------gaaggaaagtaaggtattgtgtgatttactcattttaaatccctatta-atttcttgttcattgattatttattt--cttcttt------tctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
                              ||      |      || ||     || |  || ||||| | |   | |||  |  | |  ||  | ||  |    | | |||      | |||| |  |||   |||||||||||||| |||||||| || ||||| | | ||||| | ||||| ||||| ||||| ||||| ||||| || 
gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccagattgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 4
gaaggaaagtaaggtattgtgtgatttactcattttaaa---tccctatt--aatttcttgttcattgattatttatttcttctt-ttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
     |||   |  | | |  |  |||| ||| | |||    |   || |  | ||  |  || ||| || ||  ||| ||  || |||||| | | ||| || |||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| |||||
-----aaaaacatatgtagcttatttta-tcactgtaagggttatgtactggagttgataattgatttatcatgcattactaattattctcttactctggttgtagATCTGCAGAGCGCTTGCGTATATACATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT

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|21678169|gb|BQ630520.1|BQ630520
EST:     GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG                         ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
EST: gi|151408377|gb|EV278185.1|EV278185
EST:     GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG                         ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
EST: gi|192295002|gb|FG986721.1|FG986721
EST:     GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG                         ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
EST: gi|37995772|gb|CF807361.1|CF807361
EST:     GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG                         ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttcttgttcattgattatttatttcttcttttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
                   ttatttatttcttctt  CT-rich tract
              attgattatttatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaggaaagtaaggtattgtgtgatttactcattttaaatccctattaatttcttgttcattgattatttatttcttcttttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

- - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - cttgttc