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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtattaagttccaacagcgccttcatgttataataatattgagttatggtgggcttgtggctacatcgttatactacataatgtaatggtgaaggaaggtgaatcatcgttggaatttttcttccttctaaaccttgcttgtactgttgaatctgcag

Basic information

species Zea mays
transcript GRMZM2G088212_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g51150.1 (Oryza sativa), 5'ss of exon 5
GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgta------------ttaagttccaacagcgccttcatgttataataatattg---agtta---tggtgggcttgtggctacatcgttatac-------tacataatgtaatggtgaa-----ggaaggtg-aatcatcgttggaattt--ttcttccttctaaaccttgcttgtactgttgaatctgcag
|| |||||||||||||| ||||||||| | || ||||| || ||||||||||| |||||||| |||||||||||||||||||| || ||||||||||            | || | |   |   |    | ||| |  ||  | |||    | ||   | |  | ||  | |||   | |  || |       ||  || | ||   |||       |||| ||  ||| | |    | ||||    |    || |   |||  ||| |  ||||| |  |||||
GTTAACTACTTCCCTTCAAGGTTTGATGCTGCACGTCATGCTGAGAAGGTCCCTATTCCTCCTCGTGTTCTAACAGGCTGTCGGGAAAAGgtgtgtaacttggtccacttgaactccttgcgctgttaccttgtgagcatggttttgtcccgctacattaggagactatttgctgatttggaatgcgatgaaatatgtattatagatgtggtaccctggaaagtacaatgaccacatgcatttgacacaatgttttctgcctctctttt-ttgttggaaatgcag
















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|31355364|gb|CD439721.1|CD439721
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|51592848|gb|CV071994.1|CV071994
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|166662207|gb|EG171766.1|EG171766
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGA
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGA
EST: gi|6563780|gb|AW231312.1|AW231312
EST:     CGGAGAAGGTCCCCATTCCTCNCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|213172790|gb|FM182986.1|FM182986
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGA
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|83278461|gb|DV942469.1|DV942469
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|211375390|gb|FK987875.1|FK987875
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|51592345|gb|CV071491.1|CV071491
EST:     GGAGAAGGTCCTGCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: GGAGAAGGTCC-CCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|5901194|gb|AW042294.1|AW042294
EST:     TCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: TCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|45567401|gb|CK985553.1|CK985553
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|6227062|gb|AW155766.1|AW155766
EST:     AAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: AAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|24768568|gb|CA403697.1|CA403697
EST:     AGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: AGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|60351292|gb|DN218265.1|DN218265
EST:     CCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|60348828|gb|DN215801.1|DN215801
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|37361365|gb|CF602654.1|CF602654
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAG-ATAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|60357381|gb|DN224354.1|DN224354
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|5124253|gb|AI745989.1|AI745989
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|12973094|gb|BG268309.1|BG268309
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAGCAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|6827986|gb|AW331629.1|AW331629
EST:     CGGAGAAGGTCCCCATTCCTCGCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGANCAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|24769943|gb|CA405072.1|CA405072
EST:     AGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: AGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|8930216|gb|BE224980.1|BE224980
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGA
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|31350569|gb|CD434926.1|CD434926
EST:     CGTATAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGGTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|8366919|gb|BE049927.1|BE049927
EST:     CAGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|13237225|gb|BG355239.1|BG355239
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|83279341|gb|DV943349.1|DV943349
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|16378441|gb|BI992446.1|BI992446
EST:     TCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: TCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|60342963|gb|DN209936.1|DN209936
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|38502557|gb|CF972417.1|CF972417
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
EST: gi|38502631|gb|CF972491.1|CF972491
EST:     CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAG                         TGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT
genomic: CGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtatta ... gaatctgcagTGCATCATTCAGAAGGAGAACAACTTCAAGCAGGCTGGCGAGAGATATCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTCCCCATTCCTCCCCGTGTTCTAACAGGCTGTCGTGAGAAGgtgtgtattaagttccaacagcgccttcatgttataataatattgagttatggtgggcttgtggctacatcgttatactacataatgtaatggtgaaggaaggtgaatcatcgttggaatttttcttccttctaaaccttgcttgtactgttgaatctgcag

- - - - - - - - - - - - - - - - - - - -  GGAGAA