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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtccaa--ctcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
||| | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  |||||||   | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
gta-gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtcca--actcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
    | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  ||||||  | | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
----gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
gtaagctatactcgacaacttatatattattaactttagcatttgaaattg-tacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctct--ttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                                | ||||| || |      | || || |  | | || |     | || |   |||||   |   |||||        |   |  |  ||  |  ||||| |||| ||||| |  ||  | |      | ||| |||| ||  | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
--------------------------------attttagtatgtagtggagctagttttcaagccttgacaattacttgtttgaaact-ttgtagtttagcgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
gtaagctatactcgacaacttatatat-tattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                 | || | ||| || |     |||  ||  |   |  ||    || |||| |   ||||| | || |     |    |  |      ||| ||||  |  |   |  ||||| |||| ||||| |  ||  | |     || ||| |||||||  | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
-----------------atttttgtatgtagtggagctagttttcaagccttgaca---attacttgt--ttgaaactttgtagtttagtgagtgct------aacacattgattgt---aaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                  | |     | | || |  |   ||| | ||||| | |  ||      | | |  | ||||   || | |||   | | |||    ||| ||   || || ||| |||| ||||| || || |  ||  | | |||||| |||||||||||| | |||| |||||||||||| ||||| ||||| ||||| || |||||||| ||
------------------catggccttcactaccactg--attaggaattg-attcttaag----tcatgcaatattacttaatattgctcatttgtag----actaatagttcatttgac-atatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                          ||   |  | ||     | |    ||  ||| ||   |  |||||  | |  | ||  |   | ||  | |  || ||| |   |  |  |  || ||||| ||||  | || |  ||  | | ||  || |||||||||||  | || | ||||||||||||||| || ||||| ||||||||||||||||||||
-------------------------gttccaaggtatacttagttattacgtcattggatgtttaataagtttagt-gttcatgataactgcc-tgtgatctaacac---ttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG

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|31352864|gb|CD437221.1|CD437221
EST:     ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     ATGATCTCACATTTCCTTCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                                 tttctctttcgacc  CT-rich tract
                 tatttagt  TA-rich tract