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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccattatgcctctccccgcactctcacatcgcttcctggtttcttctagggcttggcttcttgccaccgggtgcccgatctacggggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC

Basic information

species Zea mays
transcript GRMZM2G151905_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151905_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g49260.1 (Oryza sativa), 3'ss of exon 1
gtaagccattatgcctctccccgcactctcacatcgcttcctggtttcttctagggcttggcttcttgccaccgggtgcccgatctacggggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC
|||||||||| |||||| |||    | | |  ||   | |||        |||||||||||| ||| | |          ||||| | ||||    ||   || | |||  |       | ||| |     |   |  |   |||||||||||||| || ||||| |||||||| || || || || || ||||| ||||| || |||||||||||||| ||||  ||||| ||||| ||||| |
gtaagccattgtgcctccccct---cccccgtattcatccct--------ctagggcttggcctctcgtc--------ttcgatccatgggggcaatggcgca-cgcctctcagggagctaattgctgatctgatttttctccagGAGATCATCTCAGCTAGGGGTTTGGCTTGCCGTGAAGACGTGCGTCTGCTTGCCACAGTATATTTTAAGAACAGCATCAGTCGCTATTGGCGACATCGCC

upper sequence: GRMZM2G151905_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G18530.1 (Glycine max), 3'ss of exon 1
gtaagccattatgcctctccccgcactctcacatcgcttcctggtttcttctagggcttggcttcttgccaccgggtgcccgatctacggggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC
                                | || |||    | |||        | || |||   | |    ||   |  |   |   | || |  ||    |  |   | | | | | | |   |   |        ||||||  | ||  | || | ||  ||||  |  | |  |||||| ||| || | ||||| |||||||| ||||||||  |||||||||||||||| || || |
------------------------------gtaacgtttctctctctctctctctcttagggttc---cgatgaagtttgcattgcgcttagtgtttcgtttttgaggttttggcttttctgtgaatggaact--------gcagGAAGTGATTACCGCGAAGGATTTGGGGTCGCAGACGGATGTGCGCATGATGGCCACCGTGTATTTCAAGAACAGCGTCAACCGCTACTGGCGCCACCGCC

upper sequence: GRMZM2G151905_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G19490.1 (Glycine max), 3'ss of exon 1
gtaagccattatgcctctccccgcactctcacatcgcttcctggtttcttctagggcttggcttcttgccaccgggtgcccgatctacggggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC
                            | || |  ||  ||  | |||  ||||| |  |         |    ||   |  |   |   | || |  ||    |  |   | | | | | | |   |   |        ||||||  | ||  | || | ||  ||||  |  | |  |||||| ||| || | ||||| |||||||| ||||||||  |||||||||||||||| || || |
---------------------------gtaacgtttctctctc-tctctcttagggttccg---------atgaagtttgcattgcgcttagtgtttcgtttttgaggttttggcttttctgtaaatggaact--------gcagGAAGTGATTACCGCGAAGGATTTGGGGTCGCAGACGGATGTGCGCATGATGGCCACCGTGTATTTCAAGAACAGCGTCAACCGCTACTGGCGCCACCGCC

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|78107784|gb|DV526202.1|DV526202
EST:     CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTG                         GAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTC
genomic: CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTGgtaagccatt ... tgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTC
EST: gi|93282501|gb|EB674765.1|EB674765
EST:     CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTG                         GAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTC
genomic: CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTGgtaagccatt ... tgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTC
EST: gi|91051071|gb|EB161489.1|EB161489
EST:     CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTG                         GAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCCTGCT
genomic: CAGCTCTCGCGCAGTGCGAGACCCGCCCGGGCTTCTGCTCCTGCCTCCTGgtaagccatt ... tgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCC-TGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC
                                        ttttctgcttc  CT-rich tract
                          tatttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccattatgcctctccccgcactctcacatcgcttcctggtttcttctagggcttggcttcttgccaccgggtgcccgatctacggggcgtctgcttcagcacctaccgacctatttattacccggttttctgcttcgcagGAGATCATCTCGGCCAGGGGATTGGCTTGTCGGGAGGATGTCCGCCTGCTCGCCACGGTGTATTTTAAGAACAGTATCAACCGCTACTGGCGGCATCGTC

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