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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagttgaacaattttgccaagtctttgcttttatgtttcagcagatggatactctcaaaaacttgcttttgtgtttcag

Basic information

species Zea mays
transcript GRMZM2G103721_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103721_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os05g08810.1 (Oryza sativa), 5'ss of exon 15
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtag-ttagttgaacaattttgccaagtctttgcttttatgtttcagcagatggatactctcaaaaacttgcttttgtgtttcag
| ||||| || ||||| || || ||   ||| |||||||||||||| ||||| |||||  | || || |||||||||||||||||||||||||||||||||||   |  || |  || || ||    | | ||| |   |  |||  | | |  |  |   | |   || | |||          
ACGTTGATTTCGCTTTCATTCTGGGTAAAGATCCAAAGCCATTTCCACCACCAATGAAACTATGCAAAGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtaaactctttaactaacttggcgggatatctgcatgatttgttcctctgctaaaagc---cgattgctcgttttcag-------

upper sequence: GRMZM2G103721_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA06G10090.1 (Glycine max), 5'ss of exon 15
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtag----ttagttgaacaattttgccaagtcttt---gcttttatgtt-tcagcagatggatactctcaaaaacttgct----tttgtgtttcag-----
||||||| |||| |||||| ||||||||||| || ||||||||||| ||||| |||||| | || ||||||||||||||||| |||||||| || ||||||||      |  ||| |  |||      ||  |     |   || ||   || | || |  | | | | ||| | | | |    | | |||  |       
ATGTTGATTTTGGTTTTATTCTTGGGCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAGGAAATGGTTGAGGCTATGGGTGGAGCTGAAAGgtacagttctcattggatgattcactttagattcaagagtggttgtgcgatctgtagcttaa-attgtgaaatagtggttgatttctttgtccctatgcag

upper sequence: GRMZM2G103721_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA04G10090.1 (Glycine max), 5'ss of exon 15
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgta--------gttagttgaacaattttg---ccaagtctttgcttttatgtttcagcagatggatactctcaaaa--acttgcttttgtgtttcag------
||||||| |||| |||||| ||||| ||||| || ||||||||||| ||||| |||||| | || ||||||||||||||||| |||||||| || ||||||||         |||| |||   | |||     |||| || || || | || |        |  ||  |   | |   | ||| || | |||| |        
ATGTTGATTTTGGTTTTATTCTTGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAGGAAATGGTTGAGGCTATGGGTGGAGCTGAAAGgtacagttctcattagatgattcactttagattcaagactgtggttatgtgatctgtagcttaaattgtgaaatagtgatttgtttctttgttccccatgcag

upper sequence: GRMZM2G103721_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgta--gtta--gttgaacaa------ttttgccaagtctttgcttttatgtttcagcagatggatactctcaaaaacttgcttttgtgtttcag------------------------------------------------------------------------------------------
||||||| ||||  |||||  | || ||||| || ||||||||||| ||||| |||||| | || || |||||||||||||| |||||||| |||||||||||   |||   | | | ||       |||    || ||||| | || ||||| |    |    | ||     | | |   |    ||||                                                                                              
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag

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|67021489|gb|CO450238.1|CO450238
EST:     CGATGAAAGT-GTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCANAAAG                         C-AATATTACACAAGGGTCAAGTCCTACTGCTGCGAAGCATACAACATTCT
genomic: CGATGAA-GTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagtt ... tgtgtttcagCCAATATTACACAAGGTTCAAGTCCTACTGCTGCGAAGCATACAACATTCT
EST: gi|7216865|gb|AW562987.1|AW562987
EST:     CCGATGAAGTTGTGTAAGGAAATGGTTTAGGCCATGGGTGGTGCAGAAAG                         CCAATATTACACAAGGTTCAAGTCCT
genomic: CCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagtt ... tgtgtttcagCCAATATTACACAAGGTTCAAGTCCT
EST: gi|211228850|gb|FL222471.1|FL222471
EST:     AGGAAATGGTTGAGGCCATGGGTGGTGCASAAAG                         CCAATATTACACAAGGTTCAAGTCCTACTGCTGCGAAGCATACAACATTCT
genomic: AGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagtt ... tgtgtttcagCCAATATTACACAAGGTTCAAGTCCTACTGCTGCGAAGCATACAACATTCT
EST: gi|89246777|gb|DY618564.1|DY618564
EST:     CCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAG                         CCAATATTACACAAGGTTCAAGTCCTACTGCTGCGAAGCATACAACATTCT
genomic: CCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagtt ... tgtgtttcagCCAATATTACACAAGGTTCAAGTCCTACTGCTGCGAAGCATACAACATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtagttagttgaacaattttgccaagtctttgcttttatgtttcagcagatggatactctcaaaaacttgcttttgtgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA