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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctgagatgccattagatccaatcttttgagacttttgttatgttccttgtgacaaaaattcagtacatctttgctgttggtggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG

Basic information

species Zea mays
transcript GRMZM2G037200_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g45480.1 (Oryza sativa), 3'ss of exon 2
gtagctgagatgccatt-agatccaatcttttgagacttttgttatgttccttgtgacaaaaattcagtacatctttgctgt-tggtggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG
|||||||||    |||| | ||  |  |||  ||| || || |   ||||  |||||||  | || | ||| | | |||| | ||||  | ||||||||||||||||||||||  ||||| |||||| | ||||| ||||||| ||| || || |||||||||||||| || || ||||| ||||||
gtagctgaggcatcattgaaatgtacccttcagaggctcttct---gttctgtgtgacattacttta-tac-tatctgctatatggtcctgtgttagTGTGCTGGTGTCATCAATATGGGACGTGAGATCGGGTGCATGATCAGTGAGGGGCCATGGTTATTTGTTGGGATTCCAGATGCTGTGAAG

upper sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g45480.3 (Oryza sativa), 3'ss of exon 2
gtagctgagatgccatt-agatccaatcttttgagacttttgttatgttccttgtgacaaaaattcagtacatctttgctgt-tggtggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG----------
|||||||||    |||| | ||  |  |||  ||| || || |   ||||  |||||||  | || | ||| | | |||| | ||||  | ||||||||||||||||||||||  ||||| |||||| | ||||| ||||||| ||| || || |||||||||||||| || || ||||| ||||||          
gtagctgaggcatcattgaaatgtacccttcagaggctcttct---gttctgtgtgacattacttta-tac-tatctgctatatggtcctgtgttagTGTGCTGGTGTCATCAATATGGGACGTGAGATCGGGTGCATGATCAGTGAGGGGCCATGGTTATTTGTTGGGATTCCAGATGCTGTGAAGGTAGGGCGAT
















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|71297929|gb|DR784934.1|DR784934
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATT
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATT
EST: gi|149095550|gb|EE181207.2|EE181207
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|93282169|gb|EB674433.1|EB674433
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|29576800|gb|CB616912.1|CB616912
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGTTTTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|31997696|gb|CD661719.1|CD661719
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|148948214|gb|EC893730.2|EC893730
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAG
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|149086361|gb|EE175902.2|EE175902
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|26559549|gb|CA831784.1|CA831784
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|76935921|gb|DV174536.1|DV174536
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|22715752|gb|BU197942.1|BU197942
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|22819542|gb|BU499632.1|BU499632
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|29576814|gb|CB616926.1|CB616926
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGTCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGCTCGTGAGGTTGGGTGTATGATCATTTG
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGG-TCGTGAGGTTGGGTGTATGATCA-TTG
EST: gi|149070982|gb|EE159387.2|EE159387
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|211300821|gb|FL154798.1|FL154798
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|91055829|gb|EB166247.1|EB166247
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|148937590|gb|EC881777.2|EC881777
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
EST: gi|87157418|gb|DY402207.1|DY402207
EST:     CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG                         TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA
genomic: CCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAGgtagctgaga ... ggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgttccttgtgacaaaaattcagtacatctttgctgttggtggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG
               acaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctgagatgccattagatccaatcttttgagacttttgttatgttccttgtgacaaaaattcagtacatctttgctgttggtggtctgttagTGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG

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