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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accagtccatcgcccgttccgtgagcttccacaggtctatttcacccatccgtcatcctaacaaaggactactctctctcgtcctcgtcccgcctcgcagTCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCACCAAGCCGTCCGACGCCATGCGCGCCGCCATGGCCGCGGCCGACGTCGAC

Basic information

species Zea mays
transcript GRMZM2G147268_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147268_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g43650.2 (Oryza sativa), 3'ss of exon 1
-accagtccatcgcccgttccgtgagcttccacaggtctatttcacccatccgtcatcctaacaaaggactactctctctcgtcctcgtcccgcctcgcagTCGCAG----------------CACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCACCAAGCCGTCCGACGCCATGCGCGCCGCCATGGCCGCGGCCGACGTCGAC
   ||  || |  | |   |  ||  | |  |   |  ||    |  ||| |    || |   | |         |   ||  |    | | ||   ||||| | ||                ||  ||||||||||||||||||||||| |||||||||||||| || ||||| |||||||| |||||||||||||||||                
attcatgccttttcgcaaactttgcaccttaaattga-taagaaattcatgccatgtcgttttataaattcgtgttgcttccactgactactgcagtgcagTTGGAGGCTAGGAGGAGCTCCTCAAAATGGTGACCAACGTGGTGGACCTACGGTCGGACACGGTGACGAAGCCCTCCGACGCGATGCGCGCCGCCATGGC----------------

upper sequence: GRMZM2G147268_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g43650.1 (Oryza sativa), 3'ss of exon 1
-accagtccatcgcccgttccgtgagctt----ccacaggtctatttc--acccatccgtcatcctaacaaaggactactctctctcgtcctcgtcccgcctcgcagTCGCAG----------------CACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCACCAAGCCGTCCGACGCCATGCGCGCCGCCATGGCCGCGGCCGACGTCGAC
   |  | |||   || || ||  | |||    ||  |  |  ||     |  ||| |    || |   | |         |   ||  |    | | ||   ||||| | ||                ||  ||||||||||||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||||||                     
tgtccattcatg--ccttttcgcaaactttgcaccttaaattgataagaaattcatgccatgtcgttttataaattcgtgttgcttccactgactactgcagTGCAGTTGGAGGCTAGGAGGAGCTCCTCAAAATGGTGACCAACGTGGTGGACCTACGGTCGGACACGGTGACGAAGCCCTCCGACGCGATGCGCGCCGCC---------------------
















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|78111112|gb|DV529509.1|DV529509
EST:     CCACCGGTCTCGCTCTCGCAGTCCCTCGACCGCTCGTCCCGGCAGAGCAG                         TCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC
genomic: CCACCGGTCTCGCTCTCGCAGTCCCTCGACCGCTCGTCCCGGCAGAGCAGgtaggtcgtt ... cgcctcgcagTCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC
EST: gi|37416780|gb|CF646041.1|CF646041
EST:     CCACCGGTCTCGCTCTCGCAGTCCCTCGACCGCTCGTCCCGGCAGAGCAG                         TCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC
genomic: CCACCGGTCTCGCTCTCGCAGTCCCTCGACCGCTCGTCCCGGCAGAGCAGgtaggtcgtt ... cgcctcgcagTCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC
EST: gi|78115950|gb|DV534338.1|DV534338
EST:     GTCCCGGCAGAGCAG                         TCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC
genomic: GTCCCGGCAGAGCAGgtaggtcgtt ... cgcctcgcagTCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatccgtcatcctaacaaaggactactctctctcgtcctcgtcccgcctcgcagTCGCAGCACGATGGTGACCAACGTGGTGGACCTCCGGTCGGACACGGTCACCAAGCCGTCCGACGCCATGCGCGCCGCCATGGCCGCGGCCGACGTCGAC
          tcctaac  putative branch site (score: 1)
                       ctactctctctcgtcc  putative PPT
             taacaaa  TA-rich tract