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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttctgtgatttacaaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG

Basic information

species Glycine max
transcript GLYMA11G00640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G00640.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g05230.1 (Oryza sativa), 3'ss of exon 6
----------------------------gtaggtttctgtgatttacaaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG
                            ||||   ||||   |||     | ||| |  | |   |  | |      || |  |     |    ||||| ||||||  || ||||||||   |||| ||||||| || ||||||||||| ||| |||| ||||| || |||||||||||||| || || || ||||| ||||
ccttttcctgcatcattacagtacaattgtagcgctctgcactttt--ggactcatgcaactaaaaacaaacattttttattccctttctttgaatttatagGTAACGGAACAACCATCAGCTCTTGAAGGTGGGGAGTTAAGACCATATCAATTAGAGGGCCTGCAATGGATGCTTTCTTTATTCAACAATAATTTGAATG

upper sequence: GLYMA11G00640.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
---------------------------gtaggtttctgtgatttacaaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG
                            ||  | |  ||| ||      |  | |  |  | |        ||   ||||   |    |    ||||||||||||  || |||||||||  |||  ||||||| ||||| |||||||| || |||||||| ||||| |||||||||||| | ||||| |||||||| ||||
tatgcaaaaatcatattagcacaaccattaattctgcgtgtttctggtgaacctaatgtttcgcttgtgtgtgtgtttctttttttttttgc-atttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG

upper sequence: GLYMA11G00640.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097289_T03 (Zea mays), 3'ss of exon 1
----------------------gtaggtt--tctgtgatt-tacaaaattcaagagaattgtagtacaatggaattctaactagcataatt---atttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG
                       |||  |  || ||||   |    | |||  | |||  |||| |      |  | |   | |  |  ||   | |||||||| |  || ||||||||   |||  ||||||| ||||| || ||||| ||||| || || ||||| |||||||||||||||||||| |||||||| ||||
ctttgcccccttttgcaaaatcatagtgtaatcagtgaccctgtgtacttctggtgaa--gtagcaaggctaatgtttcttttgtgttctttgcacttacagGTGACAGAACAACCATCAGCTCTCGAAGGTGGGGAATTGAGGCCATATCAACTGGAGGGTCTCCAATGGATGCTTTCTTTGTTTAACAACAATTTGAATG

upper sequence: GLYMA11G00640.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0020g02960.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtaggtttctgtgatt--tacaaaattcaagagaattgtagt--acaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG
                       | |  ||   |   |  |||   |   || |||  |    |  ||||  ||||  ||   |   | |   | |  ||||||  ||||||||| |||| |||||||||||||||||||||||||||||  ||||||| || || |||||||| |||||||| ||||||||| | ||||
tttcaatgctgtgcttattgcattggtctttcattgctaatactggaaataacagatctactattaacaaaagaataatattaaatttcaaactctttagGTAACTGAGCAACCAGCTATGCTTCAAGGTGGAGAATTAAGACCATACCAGTTAGAAGGGCTTCAATGGATGCTCTCTTTGTTCAATAACAATCTGAATG

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|208181671|gb|GD974196.1|GD974196
EST:     TTGAAGGTCAGCGGCAATACAATTCTGCCATACATTCAATTCAAGAAAAG                         GTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAA
genomic: TTGAAGGTCAGCGGCAATACAATTCTGCCATACATTCAATTCAAGAAAAGgtaggtttct ... ttatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAA
EST: gi|208200749|gb|GD995196.1|GD995196
EST:     TTGAAGGTCAGCGGCAATACAATTCTGCCATACATTCAATTCAAGAAAAG                         GTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAA
genomic: TTGAAGGTCAGCGGCAATACAATTCTGCCATACATTCAATTCAAGAAAAGgtaggtttct ... ttatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG
                              ttctaac  putative branch site (score: 1)
                                     tagcataattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttctgtgatttacaaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA