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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattttctttcgtcatctcttcatatttccattaattattgtatatgttgtcttcatttatttttttttaaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0333g00010.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtaaatattt-tctttcgtcatctcttcata----tttccattaattattgtatatgttgtcttcattt--atttttttttaaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT
                      | |  ||||  |  || |  |     | | |    |||  || ||| |||     | |   | | ||||  ||| | ||  |||| |||||||| |||| ||| |||||| |||||| ||||| || |||||  |  ||||||||||||| ||  ||||||||||||| || ||||  || || || ||||
gtgaagatatttctcccaattagaagttattggttcttagctactggcttaaagggttttatatgaataatttctagtataaacatgatttcaattatattgaaaatcaacagGATGTGGAGGAGCTGATGAGTCTACCACCAGAGAAGATCTTACTTCGGTGGATGAATTTTCAACTGAAGAAAGCAGGATATAAGAGAATAGTTACAAACT

upper sequence: GLYMA03G22450.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtaaatattt-tctttcgtcatctcttcata----tttccattaattattgtatatgttgtcttcattt--atttttttttaaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT
                      | |  ||||  |  || |  |     | | |    |||  || ||| |||     | |   | | ||||  ||| | ||  |||| |||||||| |||| ||| |||||| |||||| ||||| || |||||  |  ||||||||||||| ||  ||||||||||||| || ||||  || || || ||||
gtgaagatatttctcccaattagaagttattggttcttagctactcgcttaaagggttttatatgaataatttctagtataaacatgatttcaattatattgaaaatcaacagGATGTGGAGGAGCTGATGAGTCTACCACCAGAGAAGATCTTACTTCGGTGGATGAATTTTCAACTGAAGAAAGCAGGATATAAGAGAATAGTTACAAACT

upper sequence: GLYMA03G22450.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S314_45V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------------gtaaatattttctttcg-tcatctcttcat--atttccatta-atta--ttgtatatgttgtcttcatttatttttttttaaattaac---agGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT
                                                                       | |  |  |  | || | | | |  ||  |   ||| ||||| | ||   |   ||   |   | |  || |   | || ||  | ||   ||||  | || ||| ||  || | | ||  | || ||||||||| |  ||||||||||||| ||||||| |||||| || ||||||||||| ||  | || |
gtctgtatactccctatcagtcgaagattgatcttgtttttaagttgctaccatttataacgtggttccttgaatgtggtaccgtttgattaacgtttagttagtttacattatactaaactccttacaattgttgctattgtgaatcttgaacatgacgttagGAATTTGAGGAGCTGTGGAGTATGCCAGCTGAGAAAATCTTGCTTCGGTGGATGAATTTTCATTTGAGGAAAGCGGGCTACAAGAAGATCGTGTCGAATT

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|193546295|gb|FK501772.1|FK501772
EST:     TCGATTTG-AGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|193486184|gb|FK451698.1|FK451698
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|208245262|gb|GE041628.1|GE041628
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCC-AGAAAAA-TCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|193536063|gb|FK491347.1|FK491347
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|208075796|gb|GD874753.1|GD874753
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAA
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAA
EST: gi|208188002|gb|GD986816.1|GD986816
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCT
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCT
EST: gi|193480645|gb|FK446407.1|FK446407
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAA-TCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|208276418|gb|GE076952.1|GE076952
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTAACCCCCAAGAAAAAATCTTGTTAAAGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTA-CCCCCA-GAAAAAATCTTGTTAA-GG
EST: gi|192305988|gb|FG993620.1|FG993620
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|207813907|gb|GD785142.1|GD785142
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|208261266|gb|GE058174.1|GE058174
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAA-TCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|193656419|gb|FK602891.1|FK602891
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGG
EST: gi|193419101|gb|FK382275.1|FK382275
EST:     TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAG                         GATATGGAAGAGTTGATGAATCCTACCCCCAAGAAAAAATC
genomic: TCGATTTGAAGAAAACTCCTCAGCTGCTTGAGTTGCTTGATGATAGTAAGgtaaatattt ... aaattaacagGATATGGAAGAGTTGATGAATC-TACCCCCA-GAAAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccattaattattgtatatgttgtcttcatttatttttttttaaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT
     cattaat  putative branch site (score: 3)
                                tttattttttttta  putative PPT
      attaattattgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatattttctttcgtcatctcttcatatttccattaattattgtatatgttgtcttcatttatttttttttaaattaacagGATATGGAAGAGTTGATGAATCTACCCCCAGAAAAAATCTTGTTAAGGTGGATGAATTTCCATTTGAAGAAAGCAGGGTACAAGAAGATTGTCACTAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG