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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagtaatatttaaaggggcattgctgtgttttttcgttagttaacaaaagattgtttatatgctcattgatccatcttgaccttttgcatgatatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATTGTAATCAAGACACTGATAATCACCGCAATTGGGCCTAGAGTCGGGTTAA

Basic information

species Zea mays
transcript GRMZM2G009715_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g42300.1 (Oryza sativa), 3'ss of exon 10
-taagtaatatttaaaggggcattgctgtgttttttcgttagttaacaaaagattgtttatatgctcattgatccatcttgaccttttg---catg-atatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATTGTAATCAAGACACTGATAATCACCGCAATTGGGCCTAGAGTCGGGTTAA
   |||   |||   | | |  || |||| ||| ||  ||   | |||||| || |   |      | |  | | ||||  |  |||||   ||||  |||||||||||||||||||||||||||||||||||||||||||||||| || ||||||| |||||||||| ||||||| || ||||| || || ||||| ||| |||
gacagtggcatt--gatgtgttttactgtttttctttctt---tgacaaaacatcgccgaatattccttcaacctatctcaagtttttggcccatgtgtatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGAGGCCTTATTGCAATCAAGACATTGATAATTACTGCAATAGGCCCAAGAGTTGGGCTAA

upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 11
taagtaatatttaaaggggcattgctgtgttttttcgttagtta-acaaaagattgtttatatgctcattgatccatcttgacct--tttgcatgatatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATTGTAATCAAGACACTGATAATCACCGCAATTGGGCCTAGAGTCGGGTTAA
   ||||  | | |    |||||||        |  |||| ||  ||  || | | |  |||   |   || | |||  | |  |  ||   ||  | || || ||||  | || || ||||||||||| || ||||| ||||| ||||| ||||| ||||| |||||||| || |||||||| || ||  |||| ||  | |
---gtaaactgttatactgcattgcataagaactcagttatttccactgaaaaatatg-atacatttcatg-ttcatgctcatgtggttaaaatcttttgcagGTTCTGTTTCGAGAATGGCCTAATGTCCTCTCACTCTTGGGTGGTCTGATTGTGATCAAAACACTGATTATAACCGCAATCGGTCCCCGAGTTGGCCTCA
















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|211294444|gb|FL041061.1|FL041061
EST:     TGTTGCTTGGGCTGTTCTTTGTGACTACAGGGACTTCCATTGACATGCAG                         CTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATT
genomic: TGTTGCTTGGGCTGTTCTTTGTGACTACAGGGACTTCCATTGACATGCAGgtacaattgt ... tgatatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaagattgtttatatgctcattgatccatcttgaccttttgcatgatatgtagCTTCTCATCCGGGAGTGGCCTAATGTTCTGTCACTGTTGGGGGGTCTTATTGTAATCAAGACACTGATAATCACCGCAATTGGGCCTAGAGTCGGGTTAA
                              tcttgac  putative branch site (score: 3)
      attgtttatat  TA-rich tract