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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgcttcttagtttaatgaatcatgatttagcccttctctactggaaagatgaatgtttgctatgtgatatatgcaatttttgatttgacgacaac...

Basic information

species Zea mays
transcript GRMZM2G097421_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097421_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g35570.1 (Oryza sativa), 5'ss of exon 8
ATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgcttcttagttt-aatgaatcatgatttagcccttctctactggaaagatgaatgtttgctatgtgatatatgcaatttttgat-ttgacgacaac
|||||||||||||| |||||||| ||||| ||||||||||||||| ||||||| |||||| ||||||||||||||||| |||||| |||  || || ||||||| |  |||| ||||| | | |||||    || ||  ||||    ||  ||||||||| |||| | |||| || ||     |  | || ||    |    
ATAAGCAGTATTGCTTCTGAGATCTGTGGATTTCTTACTGTGCTTTCTGGTACCGTTGTATTGCATTCTACAAGAGAATATGATCAAACTATTTCTCCAGgtaattatttctgagttttagtcaatcaatgcttggctattcttatatgagaagatgaatatttgttctgtggtacatcatgctgataatattattcatg--
















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|149013792|gb|EE043259.2|EE043259
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|149005297|gb|EE039846.2|EE039846
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|101399468|gb|EB821606.1|EB821606
EST:     TCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|78118378|gb|DV536764.1|DV536764
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|74244189|gb|DT652103.1|DT652103
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|149012853|gb|EE042695.2|EE042695
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|148947644|gb|EC893124.2|EC893124
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTGCTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|86468982|gb|DY235352.1|DY235352
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|149101363|gb|EE187480.2|EE187480
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|32939450|gb|CF044269.1|CF044269
EST:     GTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: GTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|94477225|gb|EB706183.1|EB706183
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|149070088|gb|EE158488.2|EE158488
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|44901394|gb|CK827939.1|CK827939
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|211394132|gb|FL452937.1|FL452937
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|86471099|gb|DY237469.1|DY237469
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|32940656|gb|CF045475.1|CF045475
EST:     ACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: ACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|148948890|gb|EC894304.2|EC894304
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|211094620|gb|FL143748.1|FL143748
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|94478877|gb|EB707835.1|EB707835
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|78123628|gb|DV542012.1|DV542012
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|148951156|gb|EC896835.2|EC896835
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
EST: gi|101394369|gb|EB819119.1|EB819119
EST:     TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAG                         ATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG
genomic: TACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgctt ... acaactacagATCTGTATGCTCCTCTTTCCCCAATATATTGGCATATCCAAGGTAACGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATGATCCAACCCTTACTTCAGgtaaatgcttcttagtttaatgaatcatgatttagcccttctctactggaaagatgaatgtttgctatgtgatatatgcaatttttgatttgacgacaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagatgaa