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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA

Basic information

species Zea mays
transcript GRMZM2G171406_T06
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 3
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                         |  | |   | ||| |     | || || |    ||| |   |||| |||  ||   |  ||  ||||| | | ||           ||||||||  |  |||   ||||||||||||||||||| || |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |
-------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctga-aacctggcaagaagatttgatg---------caaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43594.2 (Oryza sativa), 3'ss of exon 4
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA------------------
                         |  | |   | ||| |     | || || |    ||| |   |||| |||  ||   |  ||  ||||| | | ||           ||||||||  |  |||   ||||||||||||||||||| || |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |                  
-------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctga-aacctggcaagaagatttgatg---------caaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAAGTAAATACATGTTTCCAA

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 3
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                                                  |  |   |     |    || |    || ||        ||     | |||  |||| || | ||||||        | |||||||||||| || ||||| |||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||||||||| |
--------------------------------------------------gtccatggccttccatttcatgaccaatatttt--ctgaaacttggcaaga--aggtttgatgaaattt--------ttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA

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|71429669|gb|DR810719.1|DR810719
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|93012917|gb|EB638437.1|EB638437
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|89251407|gb|DY623193.1|DY623193
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                                       ccccatttattttc  CT-rich tract
                                           atttattttca  TA-rich tract