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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgcttttattcccataccgtggcacttttaccgtaagaatcttcgtttgccatggaggtcgattaatcagttacctctctcttgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATGCACTACCATTGCACGTTGTCAATCGGATTTTCTTGAAAAAATAGAACAT

Basic information

species Zea mays
transcript GRMZM2G124557_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124557_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 8
-------------gtgctgcttttattcccataccgtggcacttttaccgtaagaatcttcgtttgccatggaggtcgattaa--tcagttacctctctcttgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATGCACTACCATTGCACGTTGTCAATCGGATTTTCTTGAAAAAATAGAACAT--
                | ||  || ||  |||| ||    | || ||  |   ||||         | || |      |      ||||||  | || | |||||| |||||||||||| | ||||||||||| || ||||| ||  |||| |||||||| || || ||  || | |||||||| ||||||||||||| ||||  ||||||  
gtgtttatatttctaaccgcagttcttatcatagcgatata-ttatagtgcgtgaataaattgaaactatagtcccttagcggattcagttggcccttt-ttgcaa-gcagGGCTTTCACTGATGGAGTACCCTGGAGTGAAACCCATGGACCCTGCCTACGCGCTGCCGCTGGATGTTGTCAACCGGATTTTCTTGAGAAAA--GAACATTA
















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|211265935|gb|FL477027.1|FL477027
EST:     TAGGCCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAG                         GGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG
genomic: TAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAGgtgctgcttt ... tgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG
EST: gi|71443998|gb|DR825048.1|DR825048
EST:     TAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAG                         GGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG
genomic: TAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAGgtgctgcttt ... tgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG
EST: gi|89250321|gb|DY622107.1|DY622107
EST:     TAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAG                         GGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG
genomic: TAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAGgtgctgcttt ... tgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttcgtttgccatggaggtcgattaatcagttacctctctcttgcaatgcagGGCTTTCATTAATGGAGTACCCCGGGGTGAAGCCTTTGGATCCTGCCTATGCACTACCATTGCACGTTGTCAATCGGATTTTCTTGAAAAAATAGAACAT
                       gattaat  putative branch site (score: 3)
                                 ttacctctctcttgc  putative PPT
                        attaatca  TA-rich tract