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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacgagaactagagtagcaagatgaatcttgcctcttaaaaaaagtttcttttaagaaaaaataattgggctttggattaggaggtggatcaacttcatcttctattcaagctgtagcggccatacttaatggtgggtgatctgaattttcttttgtttctggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG

Basic information

species Zea mays
transcript GRMZM2G013981_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013981_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57330.1 (Oryza sativa), 3'ss of exon 2
gtgacgagaactagagtagcaagatgaatcttgcctcttaaaaaaagtttcttttaagaaaaaataattgggctttggattaggaggtggatcaacttcatctt-----ctattcaagctgtagcggccatacttaatggtggg-tgatctgaatttt--cttttgtttctgg-----aattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG
                                                                          |  ||  || |      ||| |||  |||      ||||    |  | || ||  || || |||| | |  |||| |   ||||  ||| | || |||      | ||  ||||||| ||||| |||||||  || |||||||||||||||||||| |||||||| |||||||| |||
-------------------------------------------------------------------------gtaagagaagcaaacacttcatcttgttctgtaatgctatgtgggaaggagtggtgatgctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTG

upper sequence: GRMZM2G013981_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57330.2 (Oryza sativa), 3'ss of exon 2
gtgacgagaactagagtagcaagatgaatcttgcctcttaaaaaaagtttcttttaagaaaaaataattgggctttggattaggaggtggatcaacttcatctt-----ctattcaagctgtagcggccatacttaatggtggg-tgatctgaatttt--cttttgtttctgga-----attacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG----------------------------------
                                                                          |  ||  || |      ||| |||  |||      ||||    |  | || ||  || || |||| | |  |||| |   ||||  ||| | || ||| |      ||  ||||||| ||||| |||||||  || |||||||||||||||||||| |||||||| |||||||| |||                                  
-------------------------------------------------------------------------gtaagagaagcaaacacttcatcttgttctgtaatgctatgtgggaaggagtggtgatgctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTGGTAATCTCTTCTCTTTGGACTACTGAGCTATCCT

upper sequence: GRMZM2G013981_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G08490.1 (Glycine max), 3'ss of exon 3
gtgacgagaactagagtagcaagatgaatcttgcctcttaaaaaaagtttcttttaagaaaaaataattgggctttggattaggaggtggatcaacttcatcttctattcaagctgtagcggccatacttaatggtgggtgatctgaattttcttttgtttctggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG
                                                     || |  |   ||| ||     |   |||   | ||       ||   | |||| |   |  | |   |   |||   |||    |   ||   |  ||| ||||           || ||||||| || |||||||||   ||||| || || |||||||||||| | ||||||||||||||| | 
-----------------------------------------------------ttgaagattgatactt---tctgatatttctatgt----ttgctgttttttctttcttacatat---gtttatatcaaatctctgacaattcaatctttgtttt----------ctatagGATCCCAATTCCAAGCACTTAGGGACTACAGTATGGGATGCATCACTTGTGTTTGTCAAGTTTCTT

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|211407963|gb|FL261717.1|FL261717
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|211407967|gb|FL261721.1|FL261721
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|51592994|gb|CV072140.1|CV072140
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|211407968|gb|FL261722.1|FL261722
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|211405412|gb|FL261716.1|FL261716
EST:     TCGGCTATTTCGCTTGGAGGTGATTGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: TCGGCTATTTCGC-TGGAGGTGA-TGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|211407964|gb|FL261718.1|FL261718
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
EST: gi|211405411|gb|FL261715.1|FL261715
EST:     CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAG                         GATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG
genomic: CGTCGGCTATTTCGCTGGAGGTGATGGGCCACCAGCTACATATTTCACAGgtgacgagaa ... ggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcggccatacttaatggtgggtgatctgaattttcttttgtttctggaattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG
        acttaat  putative branch site (score: 4)
                              ttttcttttgtttctg  putative PPT
                            aattttcttttgttt  TA-rich tract