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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattctttcgcatcccatgcttgcctgtttaaatgattgtttgagaaactaatctgcccgcacgcctcag

Basic information

species Zea mays
transcript GRMZM2G152573_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G05740.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattctttcgcatcccatgcttgcctgtttaaatgatt-gtttgagaaactaatctgcccgcac--gcctcag---------
|||| ||||| |||||||||||||| |||||  | || ||||  |||||||| || ||| |||||||||| ||| | ||||| | ||| || ||||||||||     ||  |   | |   |    |   | ||  ||| | | || |||   | |  | |||   ||     ||| |         
TGAGGCCTGCAGAGTACAAGAGGTCAAGGTTACCCAGAAACCGTAGGACTGTCAACCGTGCATATGGTGGAGTTTTATCTGGAAGTGCCGTCAGGGAGAGgtttgttttactagacttttaacagctatatattataataactcgtatgatttaattgtttgcttacatttatctctggttctatag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G41280.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtg-atcattctttcgcatcccatgctt--gcctgtttaaatgattgtttgagaa---actaatctgcccgcacgcctcag---------------
| || ||  | || || ||||| || |||||  | |  |||| |||||||||||| ||| |||||||||||||  ||||||| | ||| ||||| |||||||   |  ||||    | ||  |  ||   |  ||||||| |   | | ||  ||   |   |    |  ||   | |  |               
TAAGGCCAACAGAATATAAGAGATCAAGGTTACCCAAAAACCGAAGGACTGTGAACCGTGCATATGGTGGTGTGTTGTCTGGCAGTGCTGTTAGAGAGAGgtttgtttttctcaatcttcttaatctacagtatgtttaattttctttgtgcaaattgatggagtaccttgcttacttttgtctctggttctgtag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT3G28900.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattctttcgcatcccat-----gcttgcctgtttaaatgattgtttgagaaactaatctgcccgcacgcctcag
||||||||||||||||||| ||||| ||||||||||||||| | ||||| ||||||||| |||||||||||||||| |||||   ||| ||||||||||||| |   |  | |     ||  |       | |  | |||| |  ||||      |   || |||   | |  |   |||
TGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttctc-tgttccag

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|113689765|gb|DW847523.1|DW847523
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAAGGAACAGAAGATAGTGAAG
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGA-GGAACAGAAGATAGTGAAG
EST: gi|76284641|gb|DV024209.1|DV024209
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|211027947|gb|FK969517.1|FK969517
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|116826752|gb|EC870573.1|EC870573
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATACATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGAT-CATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGT
EST: gi|166675219|gb|EG147287.1|EG147287
EST:     TGGTACTGCAGTTAGGGAGAG                         GATCATTCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGT
genomic: TGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCA-TCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGT
EST: gi|88757518|gb|DY541659.1|DY541659
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTCCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|211086699|gb|FL459707.1|FL459707
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|15079950|gb|BI388889.1|BI388889
EST:     GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: GTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|60396166|gb|DN229035.1|DN229035
EST:     GCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTAGGCCGAGGAACAGAAGATAGTGAAGAAGGTATT
genomic: GCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
EST: gi|166542084|gb|EG120661.1|EG120661
EST:     CTGCAGTTAGGGAGAG                         GATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT
genomic: CTGCAGTTAGGGAGAGgtgatcattc ... cacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAGTTAGGGAGAGgtgatcattctttcgcatcccatgcttgcctgtttaaatgattgtttgagaaactaatctgcccgcacgcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG