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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag

Basic information

species Glycine max
transcript GLYMA04G03290.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 5'ss of exon 6
ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag
|||||  |  ||| ||    ||  ||  |  | ||  ||||| |||| ||||| ||||| |||||||||||||||||||||||    || ||| || |||||     |     ||| | |  |   || | ||| ||||   || || |       ||      |  ||| |    | | |   |  | || ||||||                                                            
ATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgat----accctcatc-gcctta---ttgtttca-gatg---ttcttcagtgagtgatacctattatagtatatctgatgtgtgc-gtgtt-ttttcag-----------------------------------------------------------

upper sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0004g07610.t01 (Vitis vinifera), 5'ss of exon 5
ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag
 ||||  ||||||||| |  ||| ||||| ||| ||||| |||| ||| | ||||| || ||||||||||||||||||||| ||   || || ||||||||| || || ||| ||    || | | |   ||    |  || | | |||  | | |   |||       |   | || |    | |       |||  |  |||||||               ||| || |   ||||| || ||  |  | || |||
TTGGTTCGGAACTTTAGAGGACCTCTTCTAAAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAACAAGAGAGCTGTTAAGgtgattgccaattg-atttttccaaacctatcatgttaaaacaatcgatgatgaaagagaattaatcctcctcatccagcttaaaatt-------tttggtgcaatatgtg-------------gtaaatggtgctaattt-ctcttatgatggttgtag

upper sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag
|||||  ||||||||| |  ||| |||||  || ||||| |||| ||| | ||||| || ||||||||||||||||||||||||   || || ||||||||| || || ||| ||    ||   | |   ||    |  || | | |||  | | |   |||         ||||  | ||  |   |   |||||         || | | |||        ||| || |   ||||| || ||  |  | || |||
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattg-atttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaa--------tcctcctcatccagcttaaaatttttg------gtgcaatctgt------ggtaaatggtgctaattt-ctcttatgatggttgtag

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|24205125|gb|BU964378.1|BU964378
EST:     AACATAGACCTCTGCTTTGACAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|193482421|gb|FK446176.1|FK446176
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|192334034|gb|FK026191.1|FK026191
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|58020362|gb|CX707104.1|CX707104
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|19053017|gb|BM731684.1|BM731684
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|208192105|gb|GD990639.1|GD990639
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTG
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTG
EST: gi|58016809|gb|CX703551.1|CX703551
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|192323065|gb|FK016316.1|FK016316
EST:     AACATAGACCTCTGCTTTGCCAATGAG-ATGAAGCAGCTGAACTTTTAAG                         G-ATGA-CAGAA-GATGATCCTATAGCTGCTGTAGAATTTCTTTCCAA-TA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|31462375|gb|CD404403.1|CD404403
EST:     GGATGAAGCAGCTGAACTTTTAAG                         GGATGTACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCCAATA
genomic: GGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|10848246|gb|BF070781.1|BF070781
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|22930015|gb|BU547154.1|BU547154
EST:     GCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: GCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
EST: gi|12496252|gb|BG046971.1|BG046971
EST:     AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG                         GGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA
genomic: AACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtca ... tggattttagGGATGAACAGAAAGATGATCCTATAGCTGCTGTAGAATTTCTTTCCAAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA