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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagctttttcttaatttaaattgattatgtgtttttgaagctttgaggggcttcaagctttttgtttacaacttatagaaaaaagctttttgttctaaaaataataacttcctctataacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG

Basic information

species Glycine max
transcript GLYMA20G37820.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g43800.2 (Oryza sativa), 3'ss of exon 15
gtacaagctttttcttaatttaaattgattatgtgtttttgaagctttgaggggcttcaagctttttgtttacaacttatagaaaaaagctttttgttctaaaaataataacttcctctataacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG
                               | || | ||     | ||| |   |||||  |  |  || |  | |  ||        ||        | ||| | |||  | ||   ||    ||||||      | |||  ||||||  | ||   | || | || |||||||  |  ||||||||||| || ||||||||||||| |||||||||||  || || |
------------------------------gtttgctattattattatgaag---ttcaatatggtgattgatgattcttacctt----ctccaaaggttcaaacttatatttaccctgatc-tgtgcagGACTCACTCTCTCATTGCTTATCTTCACGTTTGCTCCGTAGATGGTGCACGTTTGAATGGTTCTATAGTGCAATTGATTTTCCATGGTTTGAAAAGAGTG

upper sequence: GLYMA20G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g09760.1 (Oryza sativa), 3'ss of exon 10
gtacaagctttttcttaatttaaattgattatgtgtttttgaagctttgaggggcttcaagctttttgtttacaacttatagaaaaaagctttttgttctaaaaataataacttcctctataacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG
                                        | |           | ||||  |  | || | | ||  || ||    | || |  ||  |||   |  |  ||| || |    || | ||      |       ||||||| ||||| |     |||| ||||||| ||  | ||| ||||||||||| ||| |||||||||||||||||    | |   
----------------------------------------gtacacccaccattcatcaa--tgctagtatgccacagattgagttcaactgta-gtcttaa---ttctggcttactttcagGCTAGGAGATTGCAGC-----ATTGCTTGTCATCTGAGTCACTTCGTAGATGGTGTACATATGAGTGGTTTTACAGCGCAGTTGATTATCCATGGTTTATGGATA---

upper sequence: GLYMA20G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G314924_T01 (Zea mays), 3'ss of exon 12
gtacaagctttttcttaatttaaattgattatgtgtttttgaagctttgaggggcttcaagctttttgtttacaacttatagaaaaaagctttttgt----tctaaaaataataacttcctctataact-------tgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG
                                               |  |   |||| |  | | |  ||| |||| | | |   | | |||||||    |  || ||| | ||||     |  | ||       ||||||  ||  | |||   |||||| | ||   | || |||| || |||| ||| ||||||||||| || |||||||||||||||||||||||||| ||||| |
----------------------------------------------gtctgttacttccatttatctagtta-aactcacatagggatgttttttgtaatctgcaataatgaaaactgatatttaatctattctgatgcagGACAAACTCTCTCACTGCTTGTCCTCACGTTTGCTTCGGAGGTGGTGTATGTTTGAATGGTTCTATAGTGCAATTGATTATCCATGGTTTGCAAAAAGTG

upper sequence: GLYMA20G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G468479_T01 (Zea mays), 3'ss of exon 11
gtacaagctttttcttaatttaaattgattatgtgtttttgaagctttgaggggcttcaagctttttgtttacaacttatagaaaaaagctttttgttctaaaaataataacttcctctataacttgcagGCAAAG--GTTTCTA-GTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG
               || ||||       |||    | |  |  || | ||  |    | |     | | | |  ||  ||||      ||| || | |||||| |  | |||         |  | |||||||||  ||| ||    || ||| ||||| |     |||| |||||||  |  | ||| ||||| ||||||||| ||||||||||||||||| | || |   
--------------gtagtttatgccacctat----tatcaatactgtaagtag----agg-----tatgtcctgctcttaga------cttcttatcctaaaa-tgttgact---------atgttcagGCAAAGAAGTTGCTGCACTGTTTGTCATCTGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGTGCAGTTGATTATCCATGGTTTTCAAATA---

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|9259584|gb|BE347731.1|BE347731
EST:     CTTCTGATTACATATTGAAAAGTCAACCTAATAAGTACTCTACCCTTAAG                         GCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATT
genomic: CTTCTGATTACATATTGAAAAGTCAACCTAATAAGTACTCTACCCTTAAGgtacaagctt ... taacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATT
EST: gi|51345400|gb|CO986133.1|CO986133
EST:     CTTCTGATTACATATTGAAAAGTCAACCTAATAAGTACTCTACCCTTAAG                         GCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGNNNATT
genomic: CTTCTGATTACATATTGAAAAGTCAACCTAATAAGTACTCTACCCTTAAGgtacaagctt ... taacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatagaaaaaagctttttgttctaaaaataataacttcctctataacttgcagGCAAAGGTTTCTAGTTGCTTGGCATCTAATATGGTTCGCAGATGGTTTATTTTTGAATGGTTTTACAGTGCAATTGATTATCCATGGTTTGCCAAAAGGG
                                    cttcctctat  CT-rich tract
       aaaaaagctttttgtt  TA-rich tract