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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggagttgccttgtcgcggcttggtctaatagggttggggaatttcgttccccacctgcctttgggtgataaaaacgggatcttgttacgtcgtt...

Basic information

species Zea mays
transcript GRMZM2G144362_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g41390.4 (Oryza sativa), 5'ss of exon 2
CGCGCCGGAG-AGGCGGATCTCGGCAGGGCAG--GAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtg-gagttgccttg--tcgcggcttggtctaatagggttggggaatttcgttccccacctgcctttgggtgataaaaacgggatcttgttacg-tcgtt
   ||| ||| |||  |||   | |   || |  | || |||||||| |||||| ||||||||||||||||||| ||||||||| ||||||||||||||||||||||||| | | ||||  |  |  |  || | | || |||| |  ||     |||         ||  |  | ||  || | | |||     |   |  ||   
---GCCAGAGGAGGATGATGCGGACGCCGCGGCGGCGGCGGCGCCGAGGCACGTGTACGTGTTCCAGCGGGAGTTCGCCACGGTTGATCCGGCGCGCGTCGAGgtgcgtgcgtgatgcccgggatttcacctcgctgtagtaggttcagg---cctcgcggtttgattgggta-gtgtcgtagagatggggggggggggcactcagc
















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|76291844|gb|DV031412.1|DV031412
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|94474973|gb|EB703931.1|EB703931
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|76286746|gb|DV026314.1|DV026314
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|71441108|gb|DR822158.1|DR822158
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGTTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|78088519|gb|DV516912.1|DV516912
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|78079635|gb|DV508047.1|DV508047
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|148933496|gb|EC877205.2|EC877205
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|148981958|gb|EE028016.2|EE028016
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|91055958|gb|EB166376.1|EB166376
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|89249445|gb|DY621231.1|DY621231
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|94479450|gb|EB708408.1|EB708408
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|148985933|gb|EE029846.2|EE029846
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|149014216|gb|EE043770.2|EE043770
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|71430541|gb|DR811591.1|DR811591
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|93282998|gb|EB675262.1|EB675262
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|76937601|gb|DV175194.1|DV175194
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|93281830|gb|EB674094.1|EB674094
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|71332805|gb|DR803405.1|DR803405
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|50333623|gb|CO528749.1|CO528749
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|78123131|gb|DV541515.1|DV541515
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACGTGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|94477309|gb|EB706267.1|EB706267
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|76010683|gb|DT937853.1|DT937853
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|71449941|gb|DR830991.1|DR830991
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggagttgccttgtcgcggcttggtctaatagggttggggaatttcgttccccacctgcctttgggtgataaaaacgggatcttgttacgtcgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA