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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC

Basic information

species Glycine max
transcript GLYMA09G09430.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 3
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaa-tattaaattt---atacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
            |    |    | ||| || |  |      | || |  | |  |  | ||  |   |      |||   |||| |  ||| | |    |||||||| |||| |||||||| |||||||| || || ||||| ||||| || |||||||||||| |||||||  || |||| ||||| || || ||||||||  
-----------gtctgcacccgtcaattttcctac------gcataacctcatcacaaatatctgacgattttatttaacacaactgctaattcttcactacagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCCATTGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTTTACCAGAAGGCCA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
      | || || || |     | ||  | || |   |   |  ||  ||    || ||| ||      ||  | | || ||||  |  |   || |||||| |||| |||||||| |||||||| || || ||||| ||||| ||||||||||||||| | ||||| ||| | || ||||  | ||| ||||||||  
------gttagttccttaccttattatggttcacctggaagaatgtagcttt---tgcttaatta-----acaatatttttcaatgctgca---atgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 2
-------atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattact-tttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC----------------------------------------------------------------
        ||||   |  |  || |||   ||| || |  | |  || |    |  |||   ||| |  | | |   || || | ||     | ||  |     ||||||| |||||||||| || ||||||||||| || || || ||||| || |||||||||||| |||||||  || |||| ||||| ||||| ||||||||                                                                  
gttcgtactttactgttctgactgattgcctaaaatgat-taagcatagctggagcttat--tgagtgttgtctaaacatgcctactcc---tcttgca-----acagaggctggtttatggggccaaggcagaggctgccatcgccattggatttgatgacttcattgcagATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCAACTTGGAGATCAAGAAAGCTGACGGCAATGGTGCATTGATCGCTGAGCAAGTCTTTGAAAAGAC

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
-------atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattact-tttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
        ||||   |  |  || |||   ||| || |  | |  || |    |  |||   ||| |  | | |   || || | ||     | ||  |     ||||||| |||||||||| || ||||||||||| || || || ||||| || |||||||||||| |||||||  || |||| ||||| ||||| ||||||||  
gttcgtactttactgttctgactgattgcctaaaatgat-taagcatagctggagcttat--tgagtgttgtctaaacatgcctactcc---tcttgca-----acagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G050405_T01 (Zea mays), 3'ss of exon 3
atttaagataatttctaattaattaatattacatcaaa--attgaattattttacaatgattacttttgggcacgctttcttaca-atattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
      | | ||  |  | |  ||    || | | ||   || |    |  |   ||| ||    |   | |   ||||| |||   | ||  |   || |||||| |||||||||| || |||| |||| | || ||||| ||||| ||||||||||||||| |||||||  || |||| | ||| ||||| |||||||   
------gttcataccccactgttttg-gttgcctaaactcataggcacaactagaaattatcgaatcatgtctaactttcctacctgtcttgca---atgcagAGGCTGGTTTATGGGGCCAAGGTAGAGTCTGCCATTGCCATTGGATTCGATGACTTCATTGCAGATGCTCTGAGAGGCATTGGGTTCTACCAGAAGGATA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
      | | ||||||   ||| | | ||    |  | || ||   | | ||    |  |  |  ||    |  | |  | ||||  |  | |    |||||| |||| |||||||| |||||||| || |||||||| ||||| || ||||| |||||| | |||||  |  |||| ||||| | ||||||||||||  
------gttgatttct---taacttacatattcttcatat-gatagaatatatggagcatgttactgatagcaatcttgttcaatgctgtact---gcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
       |  || || ||  || |     |||    |||   |  | | | |  ||  | | || |    | |  | || |      ||  | || ||||||||||||||||||||| || || || ||||| || || || ||||| |||||||||||  | ||||| ||| |||| || ||  | || |||||  |  
-----gtaagatgtcgaaacaagt----ctactcacaaacccatctttctaatcatt-tcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

upper sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S21_311V6.2 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgatt--acttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
                                       || |    | |||   |  |  |   ||| | |   ||| |  |||||||  | |   |  | ||  ||||  ||  | ||  |||      |||  |||||| ||||| ||||||||| | |||||||||||| | || ||||| ||||||||||||||  | |||||| | |||||||| |     ||||| || |   
gtatagtagttgtgctatggctaaaatactaatcctttgttcacctgagtttaacaccatgtggcattcctttgtaatggtcttattttgaagtatatcaagttcggggcttgcagtgtttgaatgactt-tttgcacagAGATTGGTATATGGAGCACAAGCAGAGGCAGCACTAGCCATTGGCTTCGATGACTTCATAGCTGATGCAATTCGAGGTACAGCCCAGTATCAAAAAGTCT

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|10710429|gb|BF010120.1|BF010120
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|15000900|gb|BI321714.1|BI321714
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|4305791|gb|AI443812.1|AI443812
EST:     GTGAACCTTGCNCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|21994275|gb|BQ785803.1|BQ785803
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|6481998|gb|AW201269.1|AW201269
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|18848805|gb|BM567917.1|BM567917
EST:     GAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|254340870|gb|GR854598.1|GR854598
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|21600492|gb|BQ610823.1|BQ610823
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|7285042|gb|AW597529.1|AW597529
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|15812603|gb|BI784878.1|BI784878
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|254332221|gb|GR843805.1|GR843805
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|254317832|gb|GR826816.1|GR826816
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|192330630|gb|FK022285.1|FK022285
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
EST: gi|21993668|gb|BQ785196.1|BQ785196
EST:     GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAG                         AGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT
genomic: GTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacg ... atttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
                              ttcttac  putative branch site (score: 2)
                             tttcttacaatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG