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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtgagaactatatttttcacccgcatggaaggatagcaatgaaatgaaggggagggaaa...

Basic information

species Glycine max
transcript GLYMA07G39380.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 14
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtgagaactat--atttttcacccgcatggaaggatagcaatgaaatgaaggggagggaaa
| || | |||||| |||||||||||||| |||||||| ||||| ||||   |   | | |  |||||| |   | ||  || | || || ||  |||  |  |||  ||   ||   |    | | || |                 
GAAAGTACAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGACGgtacgaa---gcact--tctattatcaacgct--aacagtaatgtgatttatggacctttacccaaaatctcatttcatctatcatccattttcag------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 14
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 14
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtgagaactatatttttcacccgcatggaaggatagcaatgaaatgaaggggagggaaa
|||||||||||||||| |||||||| || ||||| || ||||||||||         |||  ||| | | |        | | |          |   ||| |  |   ||    |  ||  ||                     
GTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAGgta---------attagtctttagctcaaaacatatattattcttcggtttcttttcttgctaacactataa-atttcag--------------------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 14
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtga--gaactatatttttcacccgcatggaaggata-gcaatgaaatgaaggggagggaaa
|||| |||||||||||||||||||| ||||||||||| |||||||||     | ||  | | |    | ||     |     ||| | |     | | | ||  | ||   | |     | |  |||                     
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag--------------------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 14
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 14
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgta-----tatatatgtattcatctattgtttgctctgca---aaattagtgagaactatatttttcacccgcatggaaggatagcaatgaaatgaaggggagggaaa---------------------------------------------------------------------------
|||| ||||||||||||||||||||||||||||| || ||||| ||||     ||| | | |       | |  |||  ||| ||     ||||    | |  ||   ||  |  |  |   |     |||||  |       |  |                                                                                 
GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATGgtaagaagtatttctatgcatgcttgtcattttgtctccatttgtattaactcgtagaattgcttctagtcctagaaacatgcagcaaatagtcatttgctattaccccatattcatttgtttcacttgtgaatggttgtcgccccaaccaaatatgactaagcatacattttgaaatttcag

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|13788196|gb|BG650788.1|BG650788
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGTGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254342635|gb|GR858797.1|GR858797
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254342634|gb|GR858796.1|GR858796
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|298174798|gb|HO017907.1|HO017907
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|193337046|gb|FK302426.1|FK302426
EST:     CAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTTGAGGGATGAGTGGGCCCTAAAA
genomic: CAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCC-TTGAGGGATGAGTGGGCCCTAAAA
EST: gi|151402902|gb|EV272715.1|EV272715
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTACCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254318250|gb|GR832418.1|GR832418
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|193687626|gb|FK633471.1|FK633471
EST:     GTGGAGCTTGAAG                         GGGCACCCTTCAAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAA
genomic: GTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTC-AAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAA
EST: gi|58023377|gb|CX710118.1|CX710118
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254332946|gb|GR850196.1|GR850196
EST:     ACATGGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: ACATGGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|151413068|gb|EV282876.1|EV282876
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|18712744|gb|BM522681.1|BM522681
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtgagaactatatttttcacccgcatggaaggatagcaatgaaatgaaggggagggaaa

- - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - -  TTGAAG