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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCAGGCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaattttgtctagttaaatatcctgatcagaagatctttattagagtcatctcagttgtgttcttttggcctcggggacttgttccag

Basic information

species Zea mays
transcript GRMZM2G028004_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028004_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g27850.1 (Oryza sativa), 5'ss of exon 10
GTCCCAGGCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgtta--attttgtctagttaaatatcctgatcagaagat-ctttattagagtcatctc-agttgtgttcttttggcctcggggacttgtt--ccag---------------------------------------
       ||||||||||| || || |||||||| || ||  ||||||||||||| ||||| |||||||||||||| || ||||| || || |||||||||||||||||  ||||  ||||| ||||       | || || |   |  |||    | |  || || | | |||||      || | |    |||   ||                                        
-------GCAGGAGATGGTGAATGTAGCTGTGGCGGGAAGATGGTCAAAGGATTATGTGTCAAGCCAAACAAAGGAGATGCTGTGCTATTTTGGAGCATGgtgtgttataatttgttctagataaa-gcatgaaccaaaacacattccattgtcattagatccagatattttcttaaattgtcagtgctccgttagtcaactaatttcttcggcttccatgctaatttgattgtttcag

upper sequence: GRMZM2G028004_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT2G43080.1 (Arabidopsis thaliana), 5'ss of exon 11
GTCCCAGGCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaattttgtctagttaaatatcctgatcagaagatctttattagagtcatctcagttgtgttcttttggcctcggggacttgttccag
       || || ||||| || |||| |||||| || ||  |  | |||||  | | |||||| || | |||||| ||||| |||||||||||||||||||| ||||  ||   |||   |   |||     | | |  | | | | |  | |   ||   ||| ||||  ||       | |  || |||   
-------GCTGGTGATGGTGATTGCACCTGTGGTGGCAAAATCATGAAAGGCATCTCTGTTAAACCCACCAAAGGAGACGCAGTTCTCTTCTGGAGCATGgtttgtttcttcaatctctctctctatgtctct-acacaaacatgaatcaattggactgctttgagttcaattacttcttgtg--ttattcag-
















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|71440508|gb|DR821558.1|DR821558
EST:     GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTTTTTTGGAGCATG                         GGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
genomic: GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaat ... cttgttccagGGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
EST: gi|5607895|gb|AI901562.1|AI901562
EST:     GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG                         GGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
genomic: GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaat ... cttgttccagGGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
EST: gi|37381864|gb|CF627835.1|CF627835
EST:     GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG                         GGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
genomic: GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaat ... cttgttccagGGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
EST: gi|91051068|gb|EB161486.1|EB161486
EST:     GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTTTGGAGCATG                         GGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT
genomic: GATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaat ... cttgttccagGGATTGGATGGTAACACAGACCCAAACAGTATCCACAGCGGGTGCCCTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCAGGCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATGgtgtgttaattttgtctagttaaatatcctgatcagaagatctttattagagtcatctcagttgtgttcttttggcctcggggacttgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA