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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaatcttcttgtattagctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg...

Basic information

species Zea mays
transcript GRMZM2G062154_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062154_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 5'ss of exon 3
CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagtt--ctcctgaatcttcttgtattagct-ctacttatg--aattggttctga-aagtgatgtgttctggtgcaattaggtgg
|||||||||| || || |||||||||||||| ||||||||  |||| |||||||| || ||| | |||||||| |||||| |||||||||| ||||||||||||||||| | | |  | || ||||  ||| | |   |||||| ||   ||  || | ||     || || || | || |    ||   |  |  | ||      
CTGCTAGAAGGTTTAGACGTGGTCCCCATACCGAGTACATCGTATCCCTTGATGCTGATGACCTTTCACAAGGAAGCAATGCATACATGGGGAAACTGAGgtgaggttctacatggctgcatagttcactcttaatcattcttgcatattctgttattcatcctgcttagtgctaacaaattggttgcagtaatatattt------

upper sequence: GRMZM2G062154_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G35920.1 (Glycine max), 5'ss of exon 3
CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaa---tcttcttgtatt-agctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg-
| ||||| ||||  ||| ||||| ||||||||||||| || || || |||||||| || |||||||| ||||| |||||| | ||  | ||||| || |||| | | |   |    | ||| || |      ||   ||| ||| |  | || | ||   ||  | |  || | ||  | |||   |    |||   |   |   
CAGCTAGGAGATATAGGTGTGGTACCCATACTGAGTATATAATTTCACTTGATGCTGATGACTTATCCCAAGGAAGCAATGCTTATGTTGGAAAGCTAAGgtaaagctttct----tcccatagatagaaaaaaaattctgcttatggtgaggtatagacatctagtatttgt-aagataatgccattatttgcccctttttttc
















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|38687992|gb|CK145023.1|CK145023
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATAT
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATAT
EST: gi|19272436|gb|BM888692.1|BM888692
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|19058652|gb|BM737319.1|BM737319
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|74244974|gb|DT652888.1|DT652888
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|22490929|gb|BU050852.1|BU050852
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|149040587|gb|EE046828.2|EE046828
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|22490595|gb|BU050518.1|BU050518
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|87152741|gb|DY397530.1|DY397530
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|74239976|gb|DT647890.1|DT647890
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|86466002|gb|DY232375.1|DY232375
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACGTGGGAAAACTGAT                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
EST: gi|71329294|gb|DR801349.1|DR801349
EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaatcttcttgtattagctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA