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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatagtttcagttcattcagagttgttagtttcagaaccagtgttctcatctcacaaggcacaaccttttctgtatcatgatacatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA

Basic information

species Zea mays
transcript GRMZM2G152438_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 3
-------------------------gtaaccatagtttcagttcatt-cagagttg----ttagtttcagaac-----cagtgttctca-tctcacaaggcacaaccttttctgtatcatg---------atacatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
                         | ||   | |||||||||| || |  || ||    | |  |||| ||      |||  |||  | |   | | |   | |  || | |||| || |            |||||||||| ||||||||||||||||| || ||||| |||||||  || ||| ||||||
gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcaccttcacaatttctgcagacttcagagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA

upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g12830.2 (Oryza sativa), 3'ss of exon 3
-------------------------gtaaccatagtttcagttcatt-cagagttg----ttagtttcagaaccagtgt---tctca---tctcacaaggcacaaccttttctgtatcatg---------atacatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA-------------------------------------------------
                         | ||   | |||||||||| || |  || ||    | |  |||| ||    ||      |||   |   | | |   | |  || | |||| || |            |||||||||| ||||||||||||||||| || ||||| |||||||  || ||| ||||||                                                 
gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcaccttcacaatttctgcagacttcagagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAGTATCCTTCTATTATTATTGTTCAAACATACTTTTAAAGTTGCCTGCTG
















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|78077673|gb|DV506107.1|DV506107
EST:     CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAG                         GTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
genomic: CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAGgtaaccatag ... acatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
EST: gi|50328462|gb|CO523588.1|CO523588
EST:     CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAG                         GTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
genomic: CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAGgtaaccatag ... acatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
EST: gi|78122153|gb|DV540537.1|DV540537
EST:     CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAG                         GTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
genomic: CAAAGGCCGCGTGTACAACATTGCTCCATACATGAAATTTCATCCTGGAGgtaaccatag ... acatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtgttctcatctcacaaggcacaaccttttctgtatcatgatacatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
           atctcac  putative branch site (score: 3)
                                           atacattt  TA-rich tract