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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatatttccagcagagaagctattaaaagaacttataccttgtattcaaacaggcccaatattcacttcatttgctctctaattatttattgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCATTGGCTTCAGAAACTGGTGGCTTGAGTGGGAAGCCTCTCTTCAATCTCT

Basic information

species Glycine max
transcript GLYMA20G23670.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G043776_T01 (Zea mays), 3'ss of exon 7
------------------------ctatatttccagcagagaagctattaaaagaacttataccttgtattcaaacaggcccaatattcacttcatttgctctctaattat--ttattgtttc----------------tagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCATTGGCTTCAGAAACTGGTGGCTTGAGTGGGAAGCCTCTCTTCAATCTCT
                         ||| || |||    |    |||  | |||      || |||   | |  |   |  |     |||  | | | ||   |||||| |  | ||| |||                  |||||||||||||||| ||  |||| ||||||   |||||   |||| |||||||||||   ||||||||||| || |||||||||||| | ||  |  | |
gtaggttaataatcctcccacaagttattttgccatagcactgactagcataagcttgcgtaactttcttgcctatctgtgcttctctcatataaatagcgtgctaattctgctcattattttatcgacgatgaccaaacagATTATATCAAACACCACAGTTTCCAGACCATCACCTGCAGATAAACATCCATTGGCTCAGGAAACTGGTGGATTAAGTGGGAAGCCTTTGTTGGACTTAT

upper sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 7
ctatatttccagcagagaagctatta------aaagaacttataccttgtattcaaacaggcccaatattcacttcatttgc-tctctaattatttattgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCATTGGCTTCAGAAACTGGTGGCTTGAGTGGGAAGCCTCTCTTCAATCTCT
       ||||||| |||   ||| |      | |||    |    ||  |   ||  |     || || || || |||||  | | ||  | ||| || | ||||||| ||||| || || |||||||||||||||||| ||| |||  |||| ||  |||||   ||| | |||||||| ||||| ||||||||||| |||||||
-------tccagcaaagattttatcagcttgtacagattccagttgttccacagaagtattattaaaatgcaatttatttgtgtttttacattttttttttgtctagATCATATCCAATACCACCATTTCAAGACCAGATTCTGTCAGGCAAAACCCTGTGGCTGAGGAATCAGGTGGCTTAAGTGGAAAGCCTCTCTTTAATCTCT
















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|58022739|gb|CX709480.1|CX709480
EST:     GTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCNTGCCAGTAAAAATCCA
genomic: GTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
EST: gi|26058429|gb|CA801343.1|CA801343
EST:     GTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
genomic: GTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
EST: gi|17022514|gb|BM093548.1|BM093548
EST:     GTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
genomic: GTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
EST: gi|23729053|gb|BU762606.1|BU762606
EST:     TGCTGCAGTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGT-AAAATCCA
genomic: TGCTGCAGTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
EST: gi|58019265|gb|CX706007.1|CX706007
EST:     GTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
genomic: GTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
EST: gi|58016319|gb|CX703061.1|CX703061
EST:     GTTGCCTTGACTCTTCACTTGGATGGACTG                         ATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA
genomic: GTTGCCTTGACTCTTCACTTGGATGGACTGgtatctctct ... ttgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaacaggcccaatattcacttcatttgctctctaattatttattgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCATTGGCTTCAGAAACTGGTGGCTTGAGTGGGAAGCCTCTCTTCAATCTCT
                                ctctaat  putative branch site (score: 3)
                                             ttgtttct  putative PPT
                                 tctaattatttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatatttccagcagagaagctattaaaagaacttataccttgtattcaaacaggcccaatattcacttcatttgctctctaattatttattgtttctagATTATATCAAACACAACCATTTCAAGACCAGATCCTGCCAGTAAAAATCCATTGGCTTCAGAAACTGGTGGCTTGAGTGGGAAGCCTCTCTTCAATCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - ccttgta
- - - - - - - - - - - - - - - - - - - - - - - - - -caggccc