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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT

Basic information

species Glycine max
transcript GLYMA08G20100.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGA-GACCAGAGCACTT
                                                                                        ||   || || || |    ||  |    || |    ||  ||  | ||  | |||  ||       ||    |      || |||| ||||| || |||||||| ||||   |||||||||| ||||||||||| ||||| ||||||||||||   ||      |  |  ||      | ||    
---------------------------------------------------------------------------------------gtaag-ctcttctacaccggtagcatgcttaaacccaagaatt--tgatggtttcaactgataccggttcgaattttg--gtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGAACATAAAGTGTGACTAAAAATTGACCCCGGTTTAGACAGATGGGGCGAA-

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT---
                                                                                  |  | ||     ||| |  || ||   || |  |      |   | |  ||| |  | |  | ||  || |  | |  |       | |||| ||| | || ||||| || || | | | ||||||||||| ||||||||||||||||| ||||| || |    | | ||   |  ||   || ||||  |   
----------------------------------------------------------------------------------gtaagatcttaatttctactagtaccttttaatccgtgacactttatcatta-tgatgtttt-tgttttgacatctgttttggcgattcagGTGCTATTGGCTATCTAGGGTCAACTCTTTTTGTGAGGAGAATCTACAGAAACATCAAATGTGATTA-GATGATCGCAGT--TTGGAAGACATAGCAGATCAC

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaat-----gtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAG--GCTTTTGTAGGAGTC---TGAGACCAGAGCACTT
                                                                                                       | |  ||| |  || |  |  | |||  || |  ||  ||  |||  |   |||  | |||  |     ||  ||| ||||| || ||||| || || | | | ||||||||||| ||||||||||||||||| || ||||||   |||  | |     ||   || ||||| ||     
------------------------------------------------------------------------------------------------------gtgagcatttaaacttgtattcattgtatttcaaattgccacttggtctgt-tttgacaccacgtctttggtttagGTGCTGTTGGCTATCTAGGATCTACTCTCTTTGTGAGGAGAATCTACAGAAACATCAAATGCGACTAAATTGCTACTCTGAACATCAAATGTGACCAAAG-----

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtaga-gtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTG--AGACCAGAGCACTT
                                                                           || | |   ||||   ||  |||| ||  |||| | | |  || ||| |  ||||| | |  | | || ||||  |               || || ||| ||||| || ||| | || || |   | ||||||||||||||||||||||| ||||| || ||||||   |  | ||||   ||   |   |    |||  
---------------------------------------------------------------------------gtgagtcttcaaa---cttgttttcat-ctaatttcagtcttacagtggtcgtgttttgacacctttc-tatgtgt---------------atatgtagGTGCTGTTGGATATTTGGGCTCCACCCTATTTGTGAGGAGGATCTACAGAAATATCAAATGCGACTAAACTTGGTCTAGGCTGCTAGCATGTCTTGTCAC--

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT
                                                                                  |  |  |  |||| ||   | |     || |  |||| |    ||||| || || | |  | |     |   || |     || | |||||||||||| || || || || || ||| ||||||| |||||||||||||||||||||||||| |||||       |  | |      |    | | ||  |
----------------------------------------------------------------------------------gtgagctcactctcttcactctc----ttcaaactagcgagtggtgttattgatttgactaaac---cttcgttatgtgaaaattttgcagGAGCTGTTGGCTACCTGGGATCAAATCTGTTTGTAAGGAGGATCTACAGAAACATCAAGTGCGACTAGAAGAGGTAAACGGAAAAAAAGAGAAAACAAAT

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaa-atacctcttttttatattaatatta---atgctagagtagagtgttctt-aatcttatcatatggattaaatttttctccaaatgtgc-agGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT
||||||   || | | |    ||| | | |||   || | |  || ||||  |    |      |  | ||| ||   |     | | ||| || | |       |  | |||   || ||    |  | | |||||       ||     || ||   || |||||   ||   | ||||||||| || | | | || || |||||||| || |||||||||||| |||||||||| ||||||||  | |||      || |       | || |   
gtaagtagccattcttagctcaatttttttttaacttctct-ctctctctctatctctatctctctatctccctatctatccatctatatatctatctccagccgttcttttagacatccttatctgcaattttcttcgggagcattgatggggttttgttattctcttgatactctagGAGCTGTTGGGTTTTTGGGCTCCAATTTGTTCGTAAGGAGGATCTACCGAAACATCAAATGTGACTAGTGATTTGTCCAAAGGCCATTTTGATAGGATAA

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggatacctt-gtccttagtcaattgccaaatacctcttttttatatta-atattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT
                                                    |||||    ||| |||  | |||| |   |||||         ||||||||| ||   ||| ||| ||          ||  | |   | |   || |||   |||| ||| ||||| | |||||||||| || ||||| || || | |||||| || |||||||||||||||||||||||||||||||| | |   || ||||     ||  | ||      
----------------------------------------------------agaataaaaatatctttattcttattt--ttgcc--------tttttttatactatgcatttatgtta----------ttactcac--tgttgcattgat-gtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC

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|10847708|gb|BF070348.1|BF070348
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTACGAATTTGTTTCGTG-GGACGATCTAC
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTT-GTGAGGAGGATCTAC
EST: gi|193642991|gb|FK592919.1|FK592919
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGACTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
EST: gi|19935331|gb|BQ080361.1|BQ080361
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAAT-CTGTGTG                         GAGCTGTGGGGTATCTTGG
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGG
EST: gi|58015230|gb|CX701972.1|CX701972
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
EST: gi|22932835|gb|BU549974.1|BU549974
EST:     CTATTNNNNATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
EST: gi|16105838|gb|BI893578.1|BI893578
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGACTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
EST: gi|112361099|gb|EE400060.1|EE400060
EST:     CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTG                         GAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA
genomic: CTATTTTGGATACACTTTGATGTTTTGTCTTGGGCTGGGAATTCTGTGTGgtaagtcttc ... aaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT
           tcttaat  putative branch site (score: 3)
                                    tttttctcca  putative PPT
             ttaatcttatcatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggataccttgtccttagtcaattgccaaatacctcttttttatattaatattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA