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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt...

Basic information

species Glycine max
transcript GLYMA04G37810.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgta-aatcagcttgttctttagttgta---actattttccttttgctaactacaatgtattatggaact-------actatatca-------gcttgttcttcagttgtaattgtttt----------------------------
|||| | ||||||||||| |||||||| ||||||||||||||||| ||| |||| || ||||| || ||||| | |||||| |||||||| || |||| |||   |  | ||       |  |||||   ||||  |      |   |   || |  | | |  || |        || | || |       |   ||| |  |  | | ||| ||||                            
TGCTTTGATTGCTCATTTTCAGAATTCTAGCCTGATGAATGAAGACAAATGGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatatctctagtgcttattgtatacactaaatataccatatgagtgaccacttctgactgaccctattcgcacaaaatgattgacatggcggttttatacatattattattttctgataaagatacatattattattgcag

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G156956_T01 (Zea mays), 5'ss of exon 13
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt
 ||| | |||||||||||||||||||| ||||||||||||||||| ||| ||||||| ||||| || ||||| | ||||||||| || || || || | ||||   | | |  || | | |||||      |  |  |      ||  | |||| || || ||  |||    |||  | | | || ||| | ||      
CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgta---cgggtaattatcttgttgtcggcgctcgctgt------acctccatgt-ttgtgcaatgactgacgcagagt-tgcatccgttcttatcag---

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt
 |||||  |||||||||||||||| |||||  |||||||||| |||||||| ||||| ||||| ||||||||  | ||||| || ||||| || ||||  |||      ||  || |  |    |  ||||| ||  ||   | |    |    | |||      ||||      | ||  ||    |  | || |  | 
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttca--gttgtaattgtttt
 ||||| ||||||||||||||||| || ||  |||||||||| || ||||| ||||| || || ||||||||  ||||||| || ||||| || |||| ||||       || || |||| ||       ||     ||| |   |||   |||  |   |    | ||| |     ||   | ||  ||    | | || |
AGCTCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGTTGCCGCCCCATACTCTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttcttttttatttt--gtcgttggtactttccctgctatcttgttctccagttacattatgtttcgctgcagtgcactgtgacgagtcttct

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt-
 ||||||||||| ||||||||||| |||||  ||||||| ||||| ||||| ||| | |||||||||||||| || | ||| |||||||||||||||| |||||   ||        | | |||  |   || | |      ||||  |  | | ||    |   |  |||||| || ||  ||  ||  | | | |    
AGCTCTTATTGCCCATTTCCAGAACTCAAGTTTGATGAACGAAGACAAACGTTGCAGGCCTATTCTCTTCCACACTGCTGGTCCAAATGCTGGTGATCAGgtaaggaagacaagggctcaattgatatccttattcaaactataacctctttctgttgca-agtaatcatatcatctggtagttatgtattcactatagcg

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaat--------------cagcttgttctttagttgtaactattttccttttgc--taactacaatgtat-tatggaactactatatcagcttgttcttcagttgtaattgtttt--------------------------------
 ||||||||||| ||||||||||| |||||| | ||||| ||||| ||||| ||||| |||||||||||||| || ||||| |||||||||||||||| ||||||               ||  |   ||||   | ||  | ||| ||| | |||  |  || || |  |  | ||     | |||||||     ||  | |||   |   | ||                                 
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag

upper sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaa-ctattttccttttgctaactacaatgtattatggaactactatatcagcttgttct--tcagttgtaattgtttt
||||||||||||||||||||| || || ||| |||||||||| |||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||| ||||   || ||           |||   |||||||  | |||  | ||   |||||     |    |  ||||    || ||||  |  ||  | | | ||  
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttgg-atctcggatgtaaacctgtttaagaatattc-tttattctaattggtaatgactatta-

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|298176430|gb|HO026665.1|HO026665
EST:     GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
genomic: GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagc ... gtctctgcagGAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
EST: gi|9563828|gb|BE473337.1|BE473337
EST:     GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
genomic: GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagc ... gtctctgcagGAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
EST: gi|16342508|gb|BI968103.1|BI968103
EST:     GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
genomic: GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagc ... gtctctgcagGAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
EST: gi|7796615|gb|AW782012.1|AW782012
EST:     GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGNAAAAATTCGC
genomic: GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagc ... gtctctgcagGAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
EST: gi|151407718|gb|EV277533.1|EV277533
EST:     GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC
genomic: GGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagc ... gtctctgcagGAGCCTTTCCCCTTGGGTAACAATATTAGAGTGAGGCCTGGAAAAATTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG