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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCCCAGCAACCGAGCCACAGTGAGGAGGACTCGAGGGAAGAGATGGGCAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttcgagtttgcccctggtggatatcttcgcgggattccccactcgtcggcgcttgtttggatctcggccgcctaccctgccctgttcgaaatc...

Basic information

species Zea mays
transcript GRMZM2G007283_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007283_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 5'ss of exon 1
-GAGCCCCAGCAACCGAGCCACAGTGAGGAGGACTCGAGGGAAGAGATGGGCAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttcgagtttgcccctggtggatatcttcgcgggattccccactcgtcggcgcttgtttggatctcggccgcctaccctg---ccctgttcgaa--atc-
 ||| |  | | ||| | |  ||   |         |||   | |||||||||||||||| ||||| |||||||||||||||||||| |||||||| |||||||  |||    | || || | | | ||| |||| | |||||| |||  |  | |     | |  ||||   ||  |        |   | | | | | |  ||| 
AGAGGCAGACCCACC-ACCATCAACAACATCAGGAGGAGTAGATAGATGGGCAACTGCGGGACGCGAGAGGAGAATGCCGTCGTCGCGGCGCACGCCCAAGgtattcttc---gctt-cctcggattgatttcttgg-gggatttcccggtgattgttttct-taaggatgctggttgttgggatgggatctcgggttggatgatct

upper sequence: GRMZM2G007283_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 1
--GAGCCCCAGCAACCGAGCCACAGTGAGGAGGACTCGAGGGAAGAGATGGGCAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttcgagtttgcccctggtggatatcttcgcgggattccccactcgtcggcgcttgtttggatctcggccgcctaccctg---ccctgttcgaa--atc-
   || |||| || |      |   | |||||||    ||   | |||||||||||||||| ||||| ||||||||||||||||| || |||||||| |||||||  |||    | || | |    | ||| |||| | |||||| |||  |  | |    || || ||||   ||  |        |   | | | | | |  ||| 
GACAGACCCACCACCATCAAGAACATCAGGAGGAG--AAGTAGATAGATGGGCAACTGCGGGACGCGAGAGGAGAATGCCGTCGTTGCGGCGCACGCCCAAGgtattcttc---gcttcctcggatttgatttcttgg-gggatttcccggtgattgtt--ttcttgggatgctggttgttgggatgggatctcgggttggatgatct
















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|211183065|gb|FK969622.1|FK969622
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCGCAAG                         TTCAACGAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGAT
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAAC-AGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGAT
EST: gi|67022281|gb|CO451030.1|CO451030
EST:     AACTGCGGCACGCGGCGA-GAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: AACTGCGGCACGCGG-GAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|148930940|gb|EC873424.2|EC873424
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|78081509|gb|DV509921.1|DV509921
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|148932585|gb|EC876437.2|EC876437
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|211183056|gb|FK969613.1|FK969613
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCGCAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|149102573|gb|EE188233.2|EE188233
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|211183057|gb|FK969614.1|FK969614
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|71437207|gb|DR818257.1|DR818257
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|71315550|gb|DR794379.1|DR794379
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|211183058|gb|FK969615.1|FK969615
EST:     CAACTGCGGCACG-GGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|78082095|gb|DV510507.1|DV510507
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|149109789|gb|EE293582.2|EE293582
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|211396307|gb|FL093767.1|FL093767
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|149094890|gb|EE180468.2|EE180468
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|211183064|gb|FK969621.1|FK969621
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCGCAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
EST: gi|149000180|gb|EE037319.2|EE037319
EST:     CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAG                         TTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA
genomic: CAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttc ... atacttccagTTCAACAGCTCCACTTGTTACAAAATCCTGCCAAGAATGCCATTGGAGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCCCAGCAACCGAGCCACAGTGAGGAGGACTCGAGGGAAGAGATGGGCAACTGCGGCACGCGGGAGGAGAATGCCGTCGTCGCTGCGCACGCACAAGgtaccctttcgagtttgcccctggtggatatcttcgcgggattccccactcgtcggcgcttgtttggatctcggccgcctaccctgccctgttcgaaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA