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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatacccttatcacatatataagctaatataactcataagatgctgaaagcattctgaatgaaaggctgattctgggaactttgcctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGA

Basic information

species Zea mays
transcript GRMZM2G160430_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 15
---------------gtataatacccttatcacatatataagct-aatataactcat------aagatgctgaaagcatt--ctgaatgaaaggctgattc-tgggaactttgcctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGA
                 |||||        |    |  | |||| || |  | |||       | |||  |   ||||||      |||    |  || ||      |  |||  ||||  |||||||| |||||||| |||||| || | ||||||||||| ||||| || ||||||||| | || |||||||||||||||||||||||||| ||| | || |
gtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCCAACTGGCTTACATCCTTTGGAATAACAATGACAGCAAACTTGATGCTTA

upper sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
--------------------------------gtataatacccttatcacat----atataagctaatataactcataagatgctgaaagcattctgaatgaaaggctgattctgg---gaactttgcctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGA
                                || || ||   |||   |||    | ||   | | | |    ||       | |  | ||   | | | |      ||||   |    | |||||  | ||   ||||||| || |||||||||||| || | |  |||||||| ||||| |||||||||  | | || ||||  | |||||||||||||||||||||| | || |
gtataatgctttgccccatagctcacaatgatgt-tagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
















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|60349586|gb|DN216559.1|DN216559
EST:     CTGCCTTCTCCTTCGGTATGGGTTCCATTCCATGGATCATAATGTCTGAG                         ATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCC
genomic: CTGCCTTCTCCTTCGGTATGGGTTCCATTCCATGGATCATAATGTCTGAGgtataatacc ... ctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|37376279|gb|CF624650.1|CF624650
EST:     TGCCTTCTCCTTCGGTATGGGTTCCATTCC-TGGATCATAATGTTCTGAG                         ATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGC
genomic: TGCCTTCTCCTTCGGTATGGGTTCCATTCCATGGATCATAATG-TCTGAGgtataatacc ... ctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgaaagcattctgaatgaaaggctgattctgggaactttgcctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGA
                        ggctgat  putative branch site (score: 4)
                                       ctttgcct  putative PPT
                 aatgaaa  TA-rich tract