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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC

Basic information

species Zea mays
transcript GRMZM2G173428_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
gtaatatatccatatccaaccagatttcaattt-gcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
            ||      |   |   ||||  || ||   |      |  ||| |  ||  ||||| |||| |||  |  || | ||||| |||||||||||||||| ||| |||| ||||| ||||| |||||||||||||||||||| |||||||| |||||||| |||||||| || || |||||
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC

upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G14050.1 (Glycine max), 3'ss of exon 6
gtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatga--atctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
||||  |       | |  ||| || |     |||| |  |  |||||| |  ||  |   |||| ||  | | |    |  |   | |||| ||||||||||||||| |||  ||||| || ||  |||| |||||||| ||  | || || || || || |||||||||||||||||||||||||||||
gtaacgt-------tgctgccaaatgt-----tgctcatatgctgtaattattattgatatttcactgtattaagggtgttatgcctgcagAAGGTGCAAGGGCTGCTTTGAGCCTGTCTGGTACCATGCTTGGATATTACCCACTGAGAGTGCTACCTTCAAAAACTGCCATTGCACCAGTCAATCCAAC

upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 6
gtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
|||| ||  |||       ||| ||     |||||  |||||||       ||  ||  |||  ||  | |  |   |  |  || |||| ||||||||||||||| |||| ||||| |||||  |||| |||||||| ||  | || || || || ||||||||||| ||||| || || ||||||||
gtaacatgacca-------ccaaat----gtttgca-actttgtaattgttattgacatttctctgtattaacagtgttgtgcttgcagATGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTACTACCTTCGAAAACTGCTATTGCCCCTGTTAATCCAAC

upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G40750.1 (Glycine max), 3'ss of exon 5
gtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
|||| ||  |     ||||   | |    || ||||||  || | || ||    | |  || |||    || |    |  |   | |||| ||||||||||||||| |||  ||||| || ||  |||| |||||||| ||  | || || || || || ||||||||||||||||| |||||||||||
gtaacattgctg---ccaaat-gttgctcatatgcttaaattat-tattggtatttcactttatt----aacgg-tgttatgcctacagAAGGTGCAAGGGCTGCTTTGAGCCTGTCTGGTACCATGCTTGGATATTACCCATTGAGAGTGCTACCTTCAAAAACTGCCATTGCACCGGTCAATCCAAC

upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 5
gtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttc--cagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
||||  ||   | |   | | | |||  |  | |   |   |    |     |    |||| ||| |    ||   ||  | |||   |||| |||||| |||||||| ||| |||| |||| ||  |||| ||||| || ||||| ||||| |||||||| ||||| |||||||||||||| || || ||
gtaa-gtaatta-acttacctaaattctatatggtgcataattcacaggtttttggttgtttatttgactctgggtattttggttatgcagAAGGTGCACGGGCTGCTTTGAGTCTGGCAGGGACAATGCTTGGATACTACCCTGTGAGGGTGCTGCCATCTAAAACAGCCATTGCACCAGTTAACCCTAC

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|9743159|gb|BE519307.1|BE519307
EST:     GACCCAAACTCAGTCCTTCGGTTCGCGCTTCATAGAGTTCACTGATGAGG                         AGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTTGGATATTATC
genomic: GACCCAAACTCAGTCCTTCGGTTCGC-CTTCATAGAGTTCACTGATGAGGgtaatatatc ... cttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC
 tgcttac  putative branch site (score: 2)
                                           tccttgttcc  putative PPT
           taatgaat  TA-rich tract