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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT

Basic information

species Zea mays
transcript GRMZM2G423337_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
|||||   ||||  ||||||         | || |  |    | |||||||| |  | | | |     |  ||| || || |  ||| ||||||| ||||| ||||||||||| || ||||||||||| |||||||| ||||||||||| || ||||||||||| || ||||| |||||||||||||
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactat-attctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 13
--------------gtatacgatcagctagcattttcactttgtcttcttttcagctg-----tgttgttgcaccagcctcacagc-attgtattatcc-------tttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
              || | ||    | | |  |  |||  || | |       | ||      ||||  ||     |  |   |   |   |||||| |       | |||||| ||||||||||  | ||||||||||||  ||| || ||||||||||||||||||||||| || |||||||| ||||| || ||||| |   | || || |
gtaaagttatttttgtgttcgggttgttggtctgctcatcttatttaagcagtaactagtaactgttactgtgaatgatttttatttaccttattatgcaatttgatgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATTGGAGCGTGTGCACAGCTTGTGTTTGCACCTATTGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 13
-----gtatacgatcagctagcatttt-cactttgtctt-cttttcagctgtg-----ttgttgcaccagcctcacagcattgtattatcc-------tttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
     || |  ||     | || ||    | ||| | |  ||    |||| |      ||  ||    |   |    |   | |  ||| |       | |||||| |||||||||| || ||||||||||||  ||| |||||||| || |||||||||||||| || ||||| || ||||| || ||||| |   |||| || |
gtattgtgtgtgactttttggctttgcatattttatgtaactaggaagctatagctattttctgtgtgacatttgatgacctttgctatgcgacttgatgtggcagCTGTGCAGTGGAGTTGATGAAAATGCAATTGGGGCATGTGCTCAACTTGTGTTTGCACCTATTGATGAGTCCTTTGCTGATGATGCTCTGTTGCTTCCAT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 13
-----------------------gtatacg-atcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
                       || | |  |||   ||  | |   |   | |     |||    ||||    |  |  | |||      || || |  |  | || ||| |||||||||| || ||||||| ||||| ||| |||||||| || |||||||||||||| || ||||| || ||||| || ||||| |   | || || |
gtagtgtgtgtgaatttattaccgtttgcatatcttatataactaggaagctatagctattttgtgtgtgacacttgatgacccttttgttat-gtgtcttgatgtgacagCTGTGCAGTGGAGTTGATGAAAGTGCAGTTGGGGCATGTGCTCAACTTGTGTTTGCACCTATTGATGAGTCATTTGCTGATGATGCTCTGTTACTGCCAT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
--------------------gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccag----cctcacagcattgtattatcc--tttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
                    || |       | | |  || | |  || |         | ||  |||  ||     |      | ||   ||| |   ||    | |||||| ||||||||||  | ||||||||||||   || |||||||||||||||||||||||||| ||||||||||| ||||| || ||||| |   | || || |
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaacta-gttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgta------ttatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
           | | |  ||   |||||  || |       || || |  |       | |||   |||| |       | || |||    || | || || ||||| ||||||||||  | ||| |  |||||||||||||| ||||| || ||||||||||| ||||| || ||||| ||  |||| || |
-----------gtttgacttcatactttaactccaaagtttctatgctcctttgttctcttcatgacattttggattcttgattcttgtctagCTTTGTAGCGGTGTTGATGAAAATGTGGTTGGAGGTTGTGCACAGCTTGTATTTGCCCCTATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 13
---------------gtatacgatca-gctagcattttcactttgtcttcttttcag------ctgtgttgttgcaccagcctcacagcattgtat------tatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
                || |   | | |  ||   |||  |||  |||| ||   ||      || |||   |  | |    | |||  | | | |      | | || |||||| | |||||||| || ||||| |||||||||||||| ||||| ||||| || |||||||| || |||||||| ||||| || ||||| ||  |||| || |
gttggtttgtctataataaatatttatgggagtgattttgctt-atctttttcataggtagaactttgtaagtttatcttattgacataaatatttcttaaattttctgtggcagCTATGCAGTGGGGTTGATGAGAATGCAGCTGGTGCCTGTGCTCAGCTGGTTTTTGCACCTATTGATGAATCATTTGCTGATGATGCTCCTTTGCTGCCAT

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|50330290|gb|CO525416.1|CO525416
EST:     GCCTCTGCCATGACGAAGTTGTTCTGTCACGAGATATGTATCTTCTGCAG                         TTGTGCAGGGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTG
genomic: GCCTCTGCCATGACGAAGTTGTTCTGTCACGAGATATGTATCTTCTGCAGgtatacgatc ... cctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT
                         gcctcac  putative branch site (score: 3)
                                         ttatccttt  putative PPT
                                   attgtattat  TA-rich tract