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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgcttaccttcttcagatattttctttcacaactactattacttaggcgtatatcatccatgatctatccaattttgtgttgtgattcagttaaa...

Basic information

species Zea mays
transcript GRMZM2G065105_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065105_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 5'ss of exon 9
GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgcttaccttcttcagatattttctttcacaactactattacttaggcgtatatcatccatgatctatccaattttgtgttgtgattcagttaaa
|||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||| |||||| | |||||||||||||||||  || | || |||| | ||| |   ||   || |  |          || ||||   |         ||       |  | |  ||  |
GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAGgtgagtgcttagattttccatatatctgcttacctgacagttaattttggcattccattcttccactcttggaatcccttcacacaatcttaccatttca
















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|149073510|gb|EE161813.2|EE161813
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|50328477|gb|CO523603.1|CO523603
EST:     GAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGGGACATCCCTGGCTTGGCACCA
genomic: GAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|76020464|gb|DT947634.1|DT947634
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|71443470|gb|DR824520.1|DR824520
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|60340573|gb|DN207546.1|DN207546
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|89246761|gb|DY618548.1|DY618548
EST:     CCATGCNNNNNNNCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|211475623|gb|FL459214.1|FL459214
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|74237187|gb|DT645101.1|DT645101
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|60353293|gb|DN220266.1|DN220266
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|71770343|gb|DR968280.1|DR968280
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|37374830|gb|CF623807.1|CF623807
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|60356243|gb|DN223216.1|DN223216
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|5607779|gb|AI901446.1|AI901446
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|211034172|gb|FL478448.1|FL478448
EST:     CCATGCTTTTTCTCATTGTTGCCGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAAACAAGGACATTCGCGACATCCCTGGCTTGGCACC
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACAC-AACAAGGACATTCGCGACATCCCTGGCTTGGCACC
EST: gi|71314190|gb|DR793709.1|DR793709
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|148986505|gb|EE030255.2|EE030255
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|18164881|gb|BM334720.1|BM334720
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|71761831|gb|DR959768.1|DR959768
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|60394000|gb|DN226870.1|DN226870
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|78088594|gb|DV516987.1|DV516987
EST:     CCATGCNNNNNNNCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|149113113|gb|EE295877.2|EE295877
EST:     TTTTT-TCATTGTTGCGGGAGTCATAGCTATAATAATTGTTAAG                         ATTGGGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: TTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|5005565|gb|AI711627.1|AI711627
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCCCCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|14243604|gb|BG841264.2|BG841264
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
EST: gi|93282965|gb|EB675229.1|EB675229
EST:     CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG                         ATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA
genomic: CCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgctt ... attttgccagATTGTGAACCCACACAACAAGGACATTCGCGACATCCCTGGCTTGGCACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAGgtgagtgcttaccttcttcagatattttctttcacaactactattacttaggcgtatatcatccatgatctatccaattttgtgttgtgattcagttaaa

- - - - - - - - - - - - - - - - - - - - - -  GCTGGA