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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttttttcaggtgtacatattccgtgagacagatatttctggttgtgagagtataattgctttcttggttaacataaacccattttctattacaatattttatggcaaccatttttagtaaacacttttctgcttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGCGCGAAAGAATGCCAAGTTGAACGGTATCAACAATGCAACATTTGTTCAA

Basic information

species Zea mays
transcript GRMZM2G115198_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115198_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 6
gtagttttttttcaggtgtacatattccgtgaga-cagatatttctggttgtgagagtataattgctttcttggtt--------aacataaacc------cattttctattacaata----ttttatggcaaccatttttagtaaacacttttctgcttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGCGCGAAAGAATGCCAAGTTGAACGGTATCAACAATGCAACATTTGTTCAA
|||  |||| |     |   |||  |    |||| ||| |  | ||   ||||||   ||  ||  |   ||| ||        | || ||| |      ||||    |||    ||    |||  ||  || |||  |||||| |   | ||||| || |  ||||||||||||  | |||||||||||||| || ||||||||||||| ||||||   |||||| || ||| |||| ||||||| |||||| ||||||||||| 
gtaaattttctcactattatcatgctgttggagagcagttgctacta--tgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgatttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
















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|6012611|gb|AW062048.1|AW062048
EST:     GGTTTGACCCTTGCCCGAAG                         GGCAAAGCCCATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: GGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|32916675|gb|CF021487.1|CF021487
EST:     CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCCTTGCCCGAAG                         GGCGAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|78090076|gb|DV518450.1|DV518450
EST:     CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAG                         GGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|148945132|gb|EC890330.2|EC890330
EST:     CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAG                         GGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|83278825|gb|DV942833.1|DV942833
EST:     TGGAACTGGAACCATTGGTTTGACCCTTGCCTGAAG                         GGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: TGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|78109730|gb|DV528146.1|DV528146
EST:     CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAG                         GGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
EST: gi|148938312|gb|EC882620.2|EC882620
EST:     CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAG                         GGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC
genomic: CTTGATCTGTTTTGTGGAACTGGAACCATTGGTTTGACCTTTGCCCGAAGgtagtttttt ... cttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacaatattttatggcaaccatttttagtaaacacttttctgcttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGCGCGAAAGAATGCCAAGTTGAACGGTATCAACAATGCAACATTTGTTCAA
                                     cttttctgctt  CT-rich tract
                       atttttagtaaaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttttttcaggtgtacatattccgtgagacagatatttctggttgtgagagtataattgctttcttggttaacataaacccattttctattacaatattttatggcaaccatttttagtaaacacttttctgcttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGCGCGAAAGAATGCCAAGTTGAACGGTATCAACAATGCAACATTTGTTCAA

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