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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgtaaattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

Basic information

species Zea mays
transcript GRMZM2G074386_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074386_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 3
--------------------CATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgta-aattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag
                    ||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||||||       | | | ||||   |   |  ||  |  || ||  ||| ||     ||| ||| |  | ||| |||      | || |   |   |  | ||                                            
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttag--accttttgttgttatatcaatacaagaaatgata-gttgtttattgt-------------------------------------------
















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|30087523|gb|CB885729.1|CB885729
EST:     CCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: CCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|32803580|gb|CD955816.1|CD955816
EST:     GCTCTGCAGAAGAACCTAGCTGCCAGAGAATTG                         CTGTACCAACACCAGCATAATAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: GCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|149016788|gb|EE154282.2|EE154282
EST:     TTCAGGGGGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|71428371|gb|DR809421.1|DR809421
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|149088717|gb|EE177839.2|EE177839
EST:     AAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: AAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|67031178|gb|CO459927.1|CO459927
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|74239718|gb|DT647632.1|DT647632
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|19436693|gb|BM953103.1|BM953103
EST:     ATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: ATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|76013087|gb|DT940257.1|DT940257
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|40302852|gb|CK347239.1|CK347239
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|78109496|gb|DV527912.1|DV527912
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgtaaattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

- - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - AGCTGC