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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT

Basic information

species Zea mays
transcript GRMZM2G111477_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 14
----gtaat-gtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctt-tgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatcttta-attgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
    | | | |   || || | ||  |    ||||     | ||| |  | || | ||| |    | | | |  |    |  |  |||   |||||||      | |||||||  |||  | || ||||||| |||||||| ||||| |||||||| |||||||| |||||||||| ||| || ||||| ||||| ||||||||||| ||||||||||||||||||||
gtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgtacttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattaca-atacagGTGGAGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 14
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                                |  | ||    |||    |  |||| |  ||  | || ||    |||||    |  |    ||||       | |  |  | | ||||||||||||||||||||||||||||||||| |  ||| | |||||  | || || || ||||| ||||| ||||| || || || ||||| || ||||||||
-----------------------------gtagattattagcactgg---cagttgtatgcttagttctaattctatgttgttcaatcaaatttgatg------tgttgtgctttgtgcagGTGGTGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                                | |  ||  |     || |  |||| |  |   | || ||     || |    |  |    ||||       | |  |  | |  ||||||||||||||||||||||| ||||||||||  ||| | |||||  | || || || ||||| ||||| ||||| ||||| || ||||| || ||||||||
--------------------------------gtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatg------tgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                                  || |  |  || |          |||| |  |||  |||||       |||||     | ||   | || | |  | | |  || ||||||||||||||||||||| ||||||||||  ||| | |||||| | || || || ||||||| ||| ||||||||||| || || || || ||||||||
-----------------------------gtaaaatatcaactctaacagttcaatggttagttttac-aatctc-----aaatcag---atccgactttaatttgttctcgcac-tgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 14
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                                  || |  ||||| ||         |||| |  |||  |||||       |||||     | ||   | || | |  | | || |||||||||||||||||||||||| ||||| || || ||| | |||||| | || || || ||||| ||||||||||||||||| || || || || ||||||||
-----------------------------gtaaaatatcaatgctaatagttcaatggttagttttac-aatctc-----aaatcag---atccgactataatttgttctcgcat-tgcagGTGGTGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                   | | || |   |   ||  | |  |  | ||   |||  |    | ||   |  |   ||   |  || ||      ||     ||||   ||||| | |||||||||||||||||||| | ||||| ||||| || ||||| ||  |    ||||| ||||| |||||||| |||||||| ||||||||||| || ||  |
------------------gtataatctatcccaaat-ctaaaacaaaatttggttgaat--cccttaagaaaattgcgtgagaagagaat------tatattactttgtgtgtat-tacagGTGGTGGTGTTGCTCTTTTGTATGCTTCGAAAGAACTTGAGAAGCTTTCCACAGCTAACTTTGATCAGAAAATTGGTGTTCAAATCATTCAAAACGCACT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtg----ttattcctactgatctcctg---ttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                           |   | | |||| |  ||  |  |  || ||      ||  |   |||| | |||   |  |||||  ||    |||     | |       |  |  |||||||||||||||||||  | ||||| ||   ||||||||||||  | || || |||||||| ||||||||| |||| ||||||||||| |||||||| ||
---------------------------tgctgagttgtttaaacttgtacctgttttgaggaccatgtcatttgatttactgggatcacatcaa-ataatggatgagtgtttcacgggattgaatcagGTGGTGGTGTTGCTCTATTGTATGCTTCCCGGGAGCTTGATAAGATTCAAACCGCGAACTTTGATCAGAAGGTTGGAGTGCAAATCATCCAGAATGCCTT

upper sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 13
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagta-tgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
            | | || |    ||||   |   |||| |  ||   | |   |||||| ||  |      |  || ||   | | || ||| | | | | |  ||| | || ||   |||||||||||||||||||| | ||||| ||   ||||||||| ||  | || ||  | |||||||| |||||| |||| |||||||| ||||||||||| ||
------------tgggatctagcttgtt---gaattgtttacact---tgcaaatgtgttgttttttagagccatctatttagtaattaatgcgtaaca-tgaaatttgaatggat---cagGTGGTGGTGTTGCTCTTTTGTATGCTTCACGGGAGCTTGACAATGTTCAAACTTCAAACTTCGACCAGAAGGTTGGAGTGCAAATTATTCAGAATGCCTT

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|76020164|gb|DT947334.1|DT947334
EST:     TGTTGAAGAGGGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: TGTTGAAGAGGGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
EST: gi|74236027|gb|DT643941.1|DT643941
EST:     TGTTGAAGAGGGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: TGTTGAAGAGGGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
EST: gi|113703063|gb|EE680567.1|EE680567
EST:     AGATGCACTGAATGCTACTAAAGCTGCCGTTGAAGAGGGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: AGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
EST: gi|67018599|gb|CO447348.1|CO447348
EST:     GGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: GGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
EST: gi|60394542|gb|DN227412.1|DN227412
EST:     AGATGCACTGAATGCTACTAAAGCTGCCGTTGAAGAGGGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: AGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
EST: gi|211121936|gb|FL439136.1|FL439136
EST:     GGGTATTGTACCAG                         GTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA
genomic: GGGTATTGTACCAGgtaatgtatc ... gtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT
                                   atctttaattgtatat  TA-rich tract