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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA

Basic information

species Zea mays
transcript GRMZM2G030422_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatcttattat-attcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
                   |||   |   ||    || ||   | | | | |  || || | |  ||| |  |  |  | | || | ||| || ||| ||  ||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |
----------------gtgcacctgcagtttttatgctataacgatcaatattaactattggaggctacttttccttacctgttgttatttttcttcgtg--cagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA

upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatc-ttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
   ||  || || |   |  ||    || || | |    |  |  |   | |    ||| | | |  |   |   ||   || ||  | |    | |    |||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||    | ||||||||||||||||| |||||||| ||||||||||||||||
--cttatttaagctgcca--acgaggtagtt-agaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatttgttcagttattatcacagactaattga-tagccattttggtgattttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
 ||           ||||  ||| |  ||| || ||     | |    | | ||     | |      ||   | | | |||   ||   ||  |     | ||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||  | | || |||||||||||||||||||||||||| |||||||||||||
ttagccccatgtgaattaaaacaaa--aatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtat---gccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA

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|31356149|gb|CD440506.1|CD440506
EST:     ATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGAT
genomic: ATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
              aactaat  putative branch site (score: 2)
                                      ttcttattctt  putative PPT
            aaaactaatggtttta  TA-rich tract