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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggacgtacattagtctacattacattcttcttgttggtttccttgattatttatctgttattttttggttgttcacccttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC

Basic information

species Zea mays
transcript GRMZM2G048067_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 16
gtatgtggacgt---acattagtctacattacattcttcttgttgg-----------tttccttgattatttatctg-ttattttttggttgttcacccttggaat-agCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC---
|||||||| |     ||| || | ||||||||||| ||  | ||||           |||   |||||| | || || ||    ||    |||       ||| || |||||||||||||||||| | |||||||||||| ||||||||||||||||||||||| |||||| || | || ||||||||||||||||| || ||||||||   
gtatgtggccaagcaacactattttacattacatttttgctattggagttctatttatttatctgattaatgatatgcttccccttcttctgtgtgttggtggcattagcagCTTGCAAGATGACCAGCCAAATTGCTAGCTGGGATACGAGGTTTGAGTTGGGTACAAAAGCATCATTGTTGTTGCCATTTTCTCCTATTGTTGTTGCTGC

upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 15
gtatgtggac---gtacattagtctacattacattcttcttgttgg-----------tttccttgattatttatctg-ttattttttggttgttcacccttggaat-agCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC---
|||||||| |     ||| || | ||||||| ||| ||  | ||||           |||   |||||| | || || ||    ||    |||       ||| || |||||||||||||||||| | |||||||||||| ||||||||||||||||||||||| |||||| || | || ||||||||||||||||| || ||||||||   
gtatgtggcctagcaacactattttacattatatttttgctattggagttctatttatttatctgattaatgatatgcttccccttcttctgtgtgttggtggcattagcagCTTGCAAGATGACCAGCCAAATTGCTAGCTGGGATACGAGGTTTGAGTTGGGTACAAAAGCATCATTGTTGTTGCCATTTTCTCCTATTGTTGTTGCTGC
















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|30087149|gb|CB885357.1|CB885357
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
EST: gi|28576038|gb|CB281930.1|CB281930
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
EST: gi|31558447|gb|CD527659.1|CD527659
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggtttccttgattatttatctgttattttttggttgttcacccttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC
        ccttgat  putative branch site (score: 5)
                                       ttcaccctt  putative PPT
          ttgattatttatctgt  TA-rich tract