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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaagaaaaaaaaagcaggagccatgaagaattaatactcagtgctaaaaatgtggcacttctagctgacaacaatttgcaaatcatatactcctgcctgttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGACTGGATAGTGATGGCCTCCATGACCACGCACAA

Basic information

species Zea mays
transcript GRMZM5G882527_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G882527_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 4
gtaaaaaaagaaaaaaaaagcaggagccatgaagaattaatact-cagtgctaaaaatgtggcacttctagctgacaacaatttgcaaatcatatactcctgcctgttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGACTGGATAGTGATGGCCTCCATGACCACGCACAA
      | |  ||||||||  |  |      ||||| ||||||| || |  | ||||  | | ||    ||  ||  ||| |||     |  | |    ||   || |    |||||||| |||||||||||||| || |||||||||||| | ||||| || ||| |||| || |||||||||||||||||       
----gtacactaaaaaaaaataaaaa----aaagaagtaatacttcatttttgaaaactttggac----ag--gatgacattttctttgttttgt----ctatatggtg---cagTTCCTATCCATGAGGATTGCTTCAATGAGCCCAGTGTTGTATGGCTTTGGAATGGACAGCGATGGCCTCCATGACCAA------
















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|101392951|gb|EB818406.1|EB818406
EST:     CAGAACCAAGTGGAG                         TTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA
genomic: CAGAACCAAGTTGAGgtaaaaaaag ... gttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA
EST: gi|14243392|gb|BG841045.2|BG841045
EST:     ATGAGATTATCAACTATGTGCAGTCCCTGCAGAACCAAGTTGAG                         TTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA
genomic: ATGAGATTATCAACTATGTGCAGTCCCTGCAGAACCAAGTTGAGgtaaaaaaag ... gttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA
EST: gi|71769016|gb|DR966953.1|DR966953
EST:     CAGAACCAAGTTGAG                         TTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA
genomic: CAGAACCAAGTTGAGgtaaaaaaag ... gttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcacttctagctgacaacaatttgcaaatcatatactcctgcctgttttttcagTTCCTTTCCATGAGGATTGCCTCCATGAGCCCAGTGCTATATGGGTTCGGACTGGATAGTGATGGCCTCCATGACCACGCACAA
         agctgac  putative branch site (score: 3)
                                    ctcctgcctgtttttt  putative PPT
                          aaatcatata  TA-rich tract