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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatattaggcgtaataacaaagttgtcttagtggtattcttctagtattatattagcaagccttctttttgttgtgggctaatattggactccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGTCCAAGAAATGGCCCAAATTTCCGTCAAAAGGTTCTAGAGATGGGTGGCA

Basic information

species Glycine max
transcript GLYMA0084S00210.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0084S00210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 4
gaatattaggcgtaataaca-aagttgtcttagtggtattcttctagtattatattag--caagccttctttttgttgtgggctaatattg--gactccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGTCCAAGAAATGGCCCAAATTTCCGTCAAAAGGTTCTAGAGATGGGTGGCA
     | |  |  |    ||  | |  |   | |  || |    || |  | | |||    ||      | |||  ||||| |||| |||   || |   |||||||||| |||||||| ||  |  |||||||||||||||| || ||||| || ||||||||||| |||||||||||||  ||||||    |||||||||| |
-----tcacacacatcttcatgaatgattgcacttttactgacatattgctttgttaaattaaatgcattctttagtgtggactaacatttctgagtgtgtacagGTTAGGGAAATTGTAGCAGTGCTGGATCTTGATGTTCTGTTTTATCCGTGCCCAAGAAATGGTCCAAATTTCCGTCCCAAGGTTGCTCAGATGGGTGGAA
















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|151395373|gb|EV265244.1|EV265244
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|120529166|gb|EH257300.1|EH257300
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|209707530|gb|BW664989.1|BW664989
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|120495419|gb|EH223586.1|EH223586
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATT--GGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|120529421|gb|EH257555.1|EH257555
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|213604531|gb|DB970651.1|DB970651
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGGATGT-CTTTTCTATCCTTG
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTG-ATGTTCTTTTCTATCCTTG
EST: gi|20075803|gb|BQ094586.1|BQ094586
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|213601172|gb|DB964665.1|DB964665
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GNTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|21255897|gb|BQ452785.1|BQ452785
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|213618118|gb|DB965275.1|DB965275
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTANTCCTTG
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTA-TCCTTG
EST: gi|192299755|gb|FG990050.1|FG990050
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|10231986|gb|BE800874.1|BE800874
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|17519052|gb|BM188094.1|BM188094
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTG
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTG
EST: gi|17400112|gb|BM176894.1|BM176894
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|13181127|gb|BG352467.1|BG352467
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATTCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|209724769|gb|BW672551.1|BW672551
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|120494745|gb|EH222912.1|EH222912
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|213587655|gb|DB971378.1|DB971378
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
EST: gi|9902884|gb|BE611852.1|BE611852
EST:     TGAGAGCTGTCCATTTTGCCGAAAG                         GTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT
genomic: TGAGAGCTGTCCATTTTGCCGAAAGgtatggattt ... ctccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattatattagcaagccttctttttgttgtgggctaatattggactccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGTCCAAGAAATGGCCCAAATTTCCGTCAAAAGGTTCTAGAGATGGGTGGCA
                                ggctaat  putative branch site (score: 3)
                                   taatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatattaggcgtaataacaaagttgtcttagtggtattcttctagtattatattagcaagccttctttttgttgtgggctaatattggactccatacagGTTAGAGAAATTGTTGCCATTTTGGATCTTGATGTTCTTTTCTATCCTTGTCCAAGAAATGGCCCAAATTTCCGTCAAAAGGTTCTAGAGATGGGTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - -cttagtg
- - - - - - - - - - - - - - - - - - - -cttctag