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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttgaagctctgatgtaa...

Basic information

species Zea mays
transcript GRMZM2G362088_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccc-tctactcttctgagttcttatcc-ttggtt-ttctccccattccctattatcgacctgtgcatctt-cttgaagctctgatgtaa
||||||||| || ||||||||||||||||||||||||||| |||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| ||||||   |||   |||    ||| || ||||||  |||  |   ||| ||  |||  | ||    || |||     |||   | || |  ||| || |  |    
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactctttctatcttttactatgagtttgtattttttgcccgaaactgttct----

upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 5
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatctt-cttgaagctctgatgtaa-
||| || || ||||| || ||| | || || || | |||| || |||| |||||||||||||| || ||||| || |||||||||||||| ||||| |||||| | | | ||  ||  | ||   ||||   || | ||   | ||||| |      |    | | | ||    |     |  |   ||  ||   | | | 
TGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttcagttac--tgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaaaaattcccctattat

upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttga-agctctgatgtaa-
||| || || || || || ||| | || || || | |||| || |||| |||||||||||||| || ||||| || |||||||||||||| ||||| |||||| | |   ||  |   | ||   ||||   || | ||   | ||||| |      |    | | | ||    |     |     | |  ||   | | | 
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagttat--tgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat

upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctcta---ctcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttgaagctctgatgtaa-
|||  | || ||||| |||||| | |||||||  | |||  || |||| |||||||||||||| || ||||| || |  ||||||||||||||||| ||||||   | | ||         |    ||   |  |||| | |   | |  |||   | ||  | |     ||| || |   | | |  | |      ||   | 
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgtgcaatagctt----ccgagctatatctttaccaggactgaaaattagag

upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 5
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagt------ataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctg-tgcatcttcttgaagctctgatgtaa
|||  |||| |||||||||||  |||| ||||| | |||| |||| || |||||||||||||| || |||||||| | |||||||||||||||||| ||||||   |       || | |   |  || | ||   | ||||  | |||  ||   |    ||| |   || |   | || | ||| |  ||    || |       
TGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGTAGTGTATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatctttttttagtaggaagtgcaatagtattt--atttctgtttctttcttgcttaattatttctatttctttgcttgcttcatttatttatttcttttt-----

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|50330001|gb|CO525127.1|CO525127
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|211392787|gb|FL282754.1|FL282754
EST:     ATGATATAACAAGTCCGGAATCATTTAGC--ACCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|60358607|gb|DN225580.1|DN225580
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|60341032|gb|DN208005.1|DN208005
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|37401257|gb|CF637991.1|CF637991
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|60347047|gb|DN214020.1|DN214020
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|32854499|gb|CD994180.1|CD994180
EST:     TGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAATAT                         GTACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAA
genomic: TGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAA-AGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAA
EST: gi|50330000|gb|CO525126.1|CO525126
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|74243754|gb|DT651668.1|DT651668
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|161587773|gb|EY960410.1|EY960410
EST:     CGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: CGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|12968444|gb|BG265390.1|BG265390
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GCAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAA
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagG-AACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAA
EST: gi|149074254|gb|EE162627.2|EE162627
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|149078434|gb|EE167210.2|EE167210
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|74243753|gb|DT651667.1|DT651667
EST:     ATTTAGCAAAACCCAGTATTGGGTAAAG                         GAACTTCAGAAGCAGGGTAGTCCGGGTATTGTAATGGTTTGGGTTGGTAAT
genomic: ATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|149094891|gb|EE180469.2|EE180469
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|148970442|gb|EE021292.2|EE021292
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|148958503|gb|EC904742.2|EC904742
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|78091625|gb|DV519999.1|DV519999
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|78084796|gb|DV513189.1|DV513189
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|40336982|gb|CK371052.1|CK371052
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|149094892|gb|EE180470.2|EE180470
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|211392788|gb|FL282755.1|FL282755
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|18179553|gb|BM380763.1|BM380763
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|67021249|gb|CO449998.1|CO449998
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|78021899|gb|DV490286.1|DV490286
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|110201225|gb|EC883122.1|EC883122
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|60400505|gb|DN233312.1|DN233312
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|149014736|gb|EE044417.2|EE044417
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
EST: gi|13381875|gb|BG458550.1|BG458550
EST:     ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAG                         GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT
genomic: ATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtata ... cattccacagGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttgaagctctgatgtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctac