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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaaatcaatactgtaatgaactgaatcttaggatatattgccactgcaatattttttagataaatgg...

Basic information

species Zea mays
transcript GRMZM2G103897_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103897_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g45100.1 (Oryza sativa), 5'ss of exon 11
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgacc---agactgaactcttacctga-aaaatcaatact--gtaatgaactga---atcttaggatatattgccactgcaatattttttagataaatgg
||||||||||||||||| ||||||| |||||||||||||| || || ||||||||      | |   | | || |||||| | |   | | | || |||    || |||  |    ||  ||  | | |    ||  || | | || | |         
GAGTTGGCAATGATCCAAGAGAAGACCGATACTTCAGTATACCTAAGCAAgtaagccccaaaactaaatattggactctttcttaccagagttaacacttaaaaaggaatcgttctatactactagaaagaatcatagctagagttctaa---------

upper sequence: GRMZM2G103897_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G07870.1 (Glycine max), 5'ss of exon 12
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaaatcaatactgtaatgaactgaatcttaggatatattgccactgcaatattttttagataaatgg-
||||||| ||||||||  |||||||||| || ||||| |||||||||||||||||||||| |  ||      |  | |     |||  ||  | |  |    |  ||  || |   |   |  | | ||| |||  | | | |  | ||  
GAGTTGGGAATGATCCCAGAGAAGATCGTTATTTCAGCATCCCAAAACAAgtaagtagtt-ataaggagtttcaatgattcacaaatacatgattaaaccagagagatcctcaccttcactaacaaatgctataactgtaaaaatagtgtg

upper sequence: GRMZM2G103897_T03 (Zea mays), 5'ss of exon 7
lower sequence: PP1S488_10V6.1 (Physcomitrella patens), 5'ss of exon 13
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaa-atcaatactgtaatgaactgaatcttagg--atatattgccactgcaatattttttagataaatgg---------
| || ||||||||||| ||||||||||| |||||||| || ||||| || ||||| | |         ||      || |  |     |   ||   |   ||||| ||   |  |    | || |     |       | || || |  ||          
GCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAGgtaagaactcatttcttgtgtttgagtatcgaaccttgtgcgtagcttgtcgaacttaaaagtgagtcgcacatagatgtagtgtgtgatcttggaaagctgctttttgcag

upper sequence: GRMZM2G103897_T03 (Zea mays), 5'ss of exon 7
lower sequence: EFJ18278 (Selaginella moellendorffii), 5'ss of exon 12
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaaatcaatactgtaatgaactgaatcttaggatatattgccactgcaatattttttagataaatgg
| ||||| |||||||||||||||||||| |||||||| || || ||||| |||   | |    ||   |  |  || |    || |||  | |                                                         
GGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAGgtattcactctttcaatttacatcctcaa--aaacaatggaaaacag-----------------------------------------------------

upper sequence: GRMZM2G103897_T03 (Zea mays), 5'ss of exon 7
lower sequence: EFJ22017 (Selaginella moellendorffii), 5'ss of exon 12
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaaatcaatactgtaatgaactgaatcttaggatatattgccactgcaatattttttagataaatgg
| ||||| |||||||||||||||||||| |||||||| || || ||||| |||   | |    ||   |  | ||| |    || |||  | |                                                         
GGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAGgtattcactctttcaatttacattctcaa--aaacaatggaaaacag-----------------------------------------------------

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|76283830|gb|DV023398.1|DV023398
EST:     GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
genomic: GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
EST: gi|32909346|gb|CF014158.1|CF014158
EST:     AGTTGGCAATGATCCACGAGAAGATCGATACTTCAGGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
genomic: AGTTGGCAATGATCCACGAGAAGATCGATACTTCAG-TATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
EST: gi|148999289|gb|EE036219.2|EE036219
EST:     GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
genomic: GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
EST: gi|110957435|gb|EE177487.1|EE177487
EST:     GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
genomic: GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
EST: gi|16379730|gb|BI993117.1|BI993117
EST:     AATGATCCCCGAGAAGATCGATACTTCAGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
genomic: AATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA
EST: gi|13149731|gb|BG320053.1|BG320053
EST:     GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA                         GCCAAGTCATATGATCCTGAAGGGGAATACKTTGCATACTGGTTACCAGAA
genomic: GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagtt ... gtaactgcagGCCAAGTCATATGATCCTGAAGGGGAATACGTTGCATACTGGTTACCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAAgtaagtagttgaccagactgaactcttacctgaaaaatcaatactgtaatgaactgaatcttaggatatattgccactgcaatattttttagataaatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatcaa