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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC

Basic information

species Zea mays
transcript GRMZM2G114758_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114758_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g09920.2 (Oryza sativa), 3'ss of exon 5
gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                                          |||| |||      | |||| |  |   ||         |     | |    || || | |||| |||     |  ||||||    || |||       |||||||||||||||||||||||||||| | ||||||||||||| || ||| ||||||||||||||| | ||||| ||||||||||| ||||| || ||||||||||||
----------------------------------------gtacttctatatgcc-gcaaaacattactttttgaaaacatactttgcttaagtaattgttgtttgggatacagatgttactacatgcttgtta-----tcttctttcagCCCTGTTGGAACACAGTGTGTTTCCAAGGAAGATCGTCATATCGTGCAAAGAAAAGGACTTGCTGTTGTTGATTGTTCGTGGGCGCGATTAAGTGATGTC

upper sequence: GRMZM2G114758_T05 (Zea mays), 3'ss of exon 6
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttcttt--cagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                                                             | ||     || | |||  |  | |  ||       |      |  |||| |  || || ||  |  |||| ||| || |    ||  ||| || ||||| | ||| ||| | || | ||||||  ||  | |  |  |||| |||||||| ||||| ||||||||||| ||||||||| ||| |||||||
-----------------------------------------------------------gtatacctctttttactgt--atcctagggtcatttgttatgacattggatgatgtttttagtatcgtattttgagtctcatgatattggcagTCCAGTTGGTAGACAATGTGTTTCAAGGGAAGACTATGATCTGATTAAAAGGAAAGGATTAGCTGTTGTTGATTGTTCTTGGGCACGTCTAACTGATGTC
















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|4753352|gb|AI657257.1|AI657257
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTGTATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|213167931|gb|FM194811.1|FM194811
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|211480276|gb|FL093313.1|FL093313
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                          tactgat  putative branch site (score: 2)
                                ttttttagtttccttt  CT-rich tract
                             tgattttttagttt  TA-rich tract