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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaagaatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag...

Basic information

species Glycine max
transcript GLYMA08G08330.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 1
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgta-------tattatatctctgctaagt------------gtttctgaagaatgtgttggtcttcaattgtgtgattcatgtgctgagcaaca---acattctctgggcgtagagatagag--------
| |||||||| ||| ||||||||||||| ||||| || |||  ||||||||| |||||||| || ||  | || || ||||||||  | ||||| || ||||        |  |   || ||||||  |            |   |||  |  || || |||       |   ||  |   ||| |  || |       || || ||||  |   ||| | |        
TCAAGAAGATCCGCCTGGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCGCTGCTCAAGGAGATGCAGCATCGCAACATCGTCAGgtgacccacctcctccctccctgctagctccatctctctctgcggctgttggttgggtgggtgggtggattgatggattgcgtgatttgcgatttgtgaatgctttgggaatttggattgtgccgtgcag

upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G174596_T02 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaagaatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag
| |||||||| ||| | ||||||||||| ||||| || |||  ||||||||| |||||||| || ||| | || || ||||||||| | ||||| || |||||  | |  |  |   | ||  | | |   || ||       |  |   | ||    |||    |          |  || |  | |||  ||      
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCCCTCCTCAAGGAGATGCAGCACCGCAACATCGTCAGgtacgt-acgttgccagtcaggttgtgttcggagtgcaggcccccccggctatgctgctcactcac---------gcgctcccgtgccgtgcag------

upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatatt----atatctctgctaag---tgtttctgaagaatgtgt-tggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag
||||||||||  |  | |||||||||||||| || ||||| ||||| || ||  | || || || ||||||||||||||||||||||| |||||||| | ||||  |    ||| |  || | |    || ||| | |  |||  | ||||   ||||| ||  ||| ||||  |  || |||                         
TGAAGAAGATCAGGCTAGAGCAGGAGGATGAAGGTGTTCCTAGCACAGCAATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgttaataccattgttgaaaactgattcagcatgatgactctggtaaacaattttg--attgatgttttttgctacacag----------------------

upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 5'ss of exon 3
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaa-gaatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag
|||||||||| |||||||||||||| ||||| || || || ||||| || ||  | |||||||| ||||||||||| ||||| ||  | |||||||| |||||  | | |  |  |   | ||| | || | | |||  ||  | ||   ||   |  ||  |    |  |  |   | |  |||    ||  |  |||| 
TGAAGAAGATCCGCTTGGAGCAGGAAGATGAAGGAGTACCAAGCACTGCTATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcacag-tgggagtattgtgtgtgtatgtatggcttttttttttgtttccttttttgtccttttggtgatgccttcatctcctggtgtacttagat

upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: EDP08130 (Chlamydomonas reinhardtii), 5'ss of exon 2
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaag-aatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag
||||||| ||| |  ||||||||||||||||||| || || ||||| |||||||| || |||||  || | |||||  |||  |||   ||  ||||  |||      | |     | |     | |    |  | |||| ||   ||| |     || ||  | ||    | | | |   | ||                
TGAAGAAAATTAGGCTGGAGCAGGAGGATGAGGGCGTGCCTAGCACAGCCATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtcttcgcacgacactctgcgctggtgacgtgtgggcagtca-taagaggactc--gagcccgacgatatcgccccctacag------------

upper sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaagaatgtgttggtcttcaattgtgtgatt-catgtgctgagca-acaacattctctgggcgtagagatagag
|||| || || ||  ||||||| || ||||| || ||||| |||||||||||||| || ||||| ||| ||||||||||||| ||  | ||||| ||| |||| |  || ||    | |   | || |  |   || | |   || | ||| ||| ||   |    || | |  || |      ||  || ||    ||   
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtaca--atctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc

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|207704401|gb|GD686630.1|GD686630
EST:     ATTCGCAAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|208177598|gb|GD976991.1|GD976991
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGTAGT
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTG-AGT
EST: gi|298193354|gb|HO033788.1|HO033788
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|120531893|gb|EH260026.1|EH260026
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|120531742|gb|EH259875.1|EH259875
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|18038935|gb|BM307229.1|BM307229
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|7684881|gb|AW755529.1|AW755529
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|298198440|gb|HO039979.1|HO039979
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAAAGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattata ... tggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaagaatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA