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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT

Basic information

species Glycine max
transcript GLYMA06G21080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 2
-ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
      |    |   |     |||||   ||  |   |    |    ||  | ||     |     |   |   |   ||| || |    |||     ||| |||| ||||| || || ||||||||||| |||||||| |||||||| ||||||||||| || || ||||| |||||||| || |||||||| ||||| |
ccacttacatgttgcttgctgtctgtaggctc-aggctgctttcataacccactagacactatgtatatatccgactgatattactattttgatactgcagATAGCCCAAGAATACTCTGAATGTCCATCTGGAAAGAAAGGTGGAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCAT

upper sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
--ttgaaaaggataaataa--gaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
  |   |     ||  |    |||  | ||| | |    ||         |  | |||   ||   |  |  |   |    |   |||||     |||  ||||||||||||||||||||| ||||| |||||||| ||||| |||||||| ||||| ||||| || || || ||||||||||| || || ||||| ||||| |
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatga--taatagatcctgactttattttttgtact--acagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT

upper sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgaaaaggataaataagaatctgttcact-tgaaattaacctagagacaaaatattttgtccaat-tggttattatcaatagtatttcactg----act-tcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
         ||  | |||  || |||  |  | | ||  |  | || |  |  | | || |  | | |||  | | | || |  ||||   ||    ||  || ||| | |||  |||||| || || ||||||||||| || || || ||||| ||||||||||| || |||||||||||||| || ||||| || || || ||||
------gacatctacaagtttcagttttcggttagatatatttcgata-gatgtgtgttatgaattgtggagaatcttaacacgatttgtgtgtggaacgatctcagATTGCAGCAGAGTACTCTGAGTGTCCATCAGGGAAAAAAGGAGGAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCT

upper sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttca------cagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
       | ||| ||    ||||  ||||   ||  | |     ||| | || ||| | | |     |||  | | |  | |||||  ||  ||| |      ||| |||||  ||| |||||||||||||||||||| ||||||||||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||
-----ctgcatacatctccatctcatcacactaa-ctgaaaagaagatagaaaattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT

upper sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
-ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttca--cagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
     |||  ||    | ||      |  | | || ||   |     |     | ||  ||  |     | || ||   |||| |     ||   |||  ||| ||||   ||| || ||||||||||||||||| ||||| || |||||||| || |||||||| || || ||||||||||| || || ||||| || ||||
accataaaatattgccacgagcg---ttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT

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|21888702|gb|BQ741915.1|BQ741915
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|254326762|gb|GR836371.1|GR836371
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|58019562|gb|CX706304.1|CX706304
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|254317146|gb|GR826091.1|GR826091
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|9257985|gb|BE346108.1|BE346108
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|209723787|gb|BW668885.1|BW668885
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCATGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|6133782|gb|AW132175.1|AW132175
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAAGGTTGGAGACCT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAG-AAGGGTGGAGACCT
EST: gi|58021266|gb|CX708008.1|CX708008
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|254317147|gb|GR826092.1|GR826092
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|58019862|gb|CX706604.1|CX706604
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192318789|gb|FK008001.1|FK008001
EST:     ATGGTCGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|151400100|gb|EV269914.1|EV269914
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|254326763|gb|GR836372.1|GR836372
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192318790|gb|FK008002.1|FK008002
EST:     ATGGTCGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|31312264|gb|CD397467.1|CD397467
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|213614928|gb|DB957008.1|DB957008
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|151402207|gb|EV272020.1|EV272020
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192327814|gb|FK022079.1|FK022079
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|26057206|gb|CA800120.1|CA800120
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192327815|gb|FK022080.1|FK022080
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|58015222|gb|CX701964.1|CX701964
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
EST: gi|10847591|gb|BF070243.1|BF070243
EST:     ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAG                         GTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT
                                         cactgac  putative branch site (score: 2)
                       ttattatcaatagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- gaaaagga
- - - - - - aataagaa
- - - - - - - - - - - - - cacttga
- - - - - - - - - - - - - - - - - - - - - -gagacaaa