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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctagttgttgtattgatcactgaaattggaattgctttagtagctgaatatctccctccttctggtattatttactgatctcgtaactgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG

Basic information

species Glycine max
transcript GLYMA05G03730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 4
ctcctagttgttgtattgatcactgaaattggaattgctttagtagctgaatatctccctcc-ttctggtattatttactgatctcgtaactgt---tttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG
    || || | |  || |    ||   ||     || ||    | |   |||  | |  |  || |  |  | | | || ||| | ||| | |   |||| |||| ||||| ||||||||||||| |||||||||||| ||||| |||||||||| ||||
--gttaatt-tagctttcaagtttgttttttcctgtgtttggccatccatataattgctgctattattatgctttcttcttatc-cataattttctttttctagATTGAAGGAAGTGAAATTGTAGTTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
















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|209698686|gb|BW656511.1|BW656511
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
EST: gi|23056602|gb|BU577755.1|BU577755
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAG
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAG
EST: gi|209729083|gb|BW655073.1|BW655073
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
EST: gi|192306405|gb|FG997159.1|FG997159
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGT
EST: gi|6455321|gb|AW186004.1|AW186004
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
EST: gi|120496159|gb|EH224326.1|EH224326
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGTTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
EST: gi|209729478|gb|BW655108.1|BW655108
EST:     CCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: CCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
EST: gi|209698687|gb|BW656512.1|BW656512
EST:     AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAG                         ATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT
genomic: AACCAATTATGAGTGACAAAGAGTTTGATGAGTTGAAACTGAGGCTAAAGgtttgctatt ... tgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgaatatctccctccttctggtattatttactgatctcgtaactgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG
                                      tcgtaac  putative branch site (score: 2)
                                            ctgttttcc  CT-rich tract
                       tattatttactgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctagttgttgtattgatcactgaaattggaattgctttagtagctgaatatctccctccttctggtattatttactgatctcgtaactgttttccagATAGAAGGGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - gttgttg
- - - - - - - - - - cactgaa
- - - - - - - - - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - gtagctg