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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctaagcttggtttgtgtggagtccgtcctcagattttaattttccacctttcaattttactgataaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA

Basic information

species Zea mays
transcript GRMZM2G005849_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 10
--------gtttgtctaa--gcttggtttgtgtggagtccgt--cctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA
         ||  |  ||  | ||  |||      | |||    | ||   || |  |||  ||  | |    ||||||    |||||| |   ||||||||| || | ||||| ||||||| ||||||||||| ||||| || ||||| || || || ||||||||||||||||| ||||| ||||| || || |  | || ||    |   |
gtttgcacattctttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtgttgttatttgttcg-ttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 10
-------gtttgtctaa---gcttggtttgtgtggagtccgt--cctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA
         |||| | |   | ||  |||      | |||    | ||   || |  |||  ||  | |    ||||||    |||||| |  |||||||||| ||   ||||| ||||||| ||||||||||| ||||| || ||||| || || || ||||||||||||||||| ||||| ||||| || || |  | || ||    |   |
gtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttcc-ttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA
















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|7216484|gb|AW562606.1|AW562606
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|89248870|gb|DY620656.1|DY620656
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTGGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|148955139|gb|EC900656.2|EC900656
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTGGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|71771453|gb|DR969390.1|DR969390
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|149005283|gb|EE039832.2|EE039832
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|74242021|gb|DT649935.1|DT649935
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|211029256|gb|FL478423.1|FL478423
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|86855990|gb|DY307001.1|DY307001
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCCCGCGTACCATCTGACTGTTCTCCAGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|149014771|gb|EE044463.2|EE044463
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
EST: gi|113842557|gb|DW969340.1|DW969340
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTACTCCGGGGATTCG
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTT-CTCCGGGGATTCG
EST: gi|111197488|gb|EE295623.1|EE295623
EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaattttccacctttcaattttactgataaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA
                         tactgat  putative branch site (score: 2)
                                      ttatttcttt  putative PPT
                tttcaattttactgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctaagcttggtttgtgtggagtccgtcctcagattttaattttccacctttcaattttactgataaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG