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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactgttccatctgatcgtcagtaggac...

Basic information

species Zea mays
transcript GRMZM5G860137_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 12
ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactg-----ttccatctgatcgtcagtaggac----------------------------------------------------------------------------------------------
||||||||||| |||||||||||  |||| |||||||||||||||||||| || || || ||||| ||||| ||| |||| ||||||||||  | || | | ||| || |||     |  | | |      |||||  ||||   ||||| | | |  |||||     |    | |  |  |  ||| |                                                                                                
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatg--cagttatttgttgtactgattattcatgtatagttttgtgtaagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag

upper sequence: GRMZM5G860137_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g02020.3 (Oryza sativa), 5'ss of exon 11
ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactgt---tccatctgatcgtcagtaggac
||||||||||| |||||||||||  |||| |||||||||||||||||||| || || || ||||| ||||| ||| |||| ||||||||||  | || | | ||| || |||     |  | | |      |||||  ||||   ||||| | | |  |||||    | ||| |     |  ||   | 
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatg--cagttatttgttgtactgattattcatgtatagttttgtgtaa-
















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|71442413|gb|DR823463.1|DR823463
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGTTCAT                         GCAACCCTTTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|71426142|gb|DR807192.1|DR807192
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|21891396|gb|BQ744609.1|BQ744609
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|93281947|gb|EB674211.1|EB674211
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|211211417|gb|FL472067.1|FL472067
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|149110542|gb|EE294180.2|EE294180
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGTTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|60353947|gb|DN220920.1|DN220920
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|110951057|gb|EE171162.1|EE171162
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|110202377|gb|EC884274.1|EC884274
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|149107170|gb|EE189057.2|EE189057
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|78544790|gb|DV622288.1|DV622288
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|71437289|gb|DR818339.1|DR818339
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|89760641|gb|DY688973.1|DY688973
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|71298332|gb|DR785147.1|DR785147
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|91051494|gb|EB161912.1|EB161912
EST:     GGGGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGTTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|88748462|gb|DY532603.1|DY532603
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|71763804|gb|DR961741.1|DR961741
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|37375775|gb|CF624352.1|CF624352
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCTTATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|78544465|gb|DV621963.1|DV621963
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|60353407|gb|DN220380.1|DN220380
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTTTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|211357448|gb|FL362295.1|FL362295
EST:     GGAGTTTGCAATGGCAGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|74232956|gb|DT640870.1|DT640870
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|6865254|gb|AW360604.1|AW360604
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|78078472|gb|DV506885.1|DV506885
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGTTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|50322371|gb|CO517497.1|CO517497
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|149029956|gb|EE154793.2|EE154793
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGTTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|149087111|gb|EE176650.2|EE176650
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|20337069|gb|BQ172699.1|BQ172699
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|113701695|gb|EE679199.1|EE679199
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGCGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
EST: gi|110939957|gb|EE160114.1|EE160114
EST:     GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT                         GCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT
genomic: GGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctctt ... catgatgcagGCAACCCTCTTCGCATATCCATTCATCATTGTGAAGTTGGTGCGAGCAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactgttccatctgatcgtcagtaggac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA