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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag

Basic information

species Zea mays
transcript GRMZM5G844195_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 19
GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattct-----tgttttatggctagttcat-ttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag
|||||| |||||||||||||| || |||||||| |||||||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||||||||  |||       |||||  |   |   | || ||   |     || | |  ||  || |  |    |||  || | | | | | | | |  || | ||  |     |  |  ||||                                                                   
GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgca-cataataacatcctgctgaataattgtgcag------------------------------------------------------------------

upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ27365 (Selaginella moellendorffii), 5'ss of exon 17
GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag
 || || ||||| ||||| |||||||| || |||||  | ||| | |  | | | |||||||| ||||| |||||||| |||||||||||  | ||||||||||    | |  |  ||     ||  |   || | |||    | |  | ||                                                                                                                                 
AGCACAAATCACGGCAATGCACCTGATCATCGGGACATTGCAGAGAACTACTGTCTTTGGGGTAGAAAACAGAGACACGCTCACTCACAAAGCTACAGGGgtaa--gctttgctcgtactttcagaccgaatctcactc---tcgctttgcag--------------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ33136 (Selaginella moellendorffii), 5'ss of exon 17
GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag
 || || ||||| ||||| |||||||| || |||||  | ||| | |  | | | |||||||| ||||| |||||||| |||||||||||  | ||||||||||    | |  |  ||     ||  |   || | |||  || | | | ||                                                                                                                                 
AGCACAAATCACGGCAATGCACCTGATCATCGGGACATTGCAGAGAACTACTGTCTTTGGGGTAGAAAACAGAGACACGCTCACTCACAAAGCTACAGGGgtaa--gctttgctcgtactttcagaccgaatctcactc--tcgctcttgcag--------------------------------------------------------------------------------------------------------------------------------

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|31356855|gb|CD441212.1|CD441212
EST:     ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTCTATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|67012219|gb|CO440968.1|CO440968
EST:     ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211321315|gb|FL043264.1|FL043264
EST:     ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|18964320|gb|BM660937.1|BM660937
EST:     ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTCTATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211321314|gb|FL043263.1|FL043263
EST:     ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|67014984|gb|CO443733.1|CO443733
EST:     ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211321316|gb|FL043265.1|FL043265
EST:     ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211321311|gb|FL043260.1|FL043260
EST:     ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211321310|gb|FL043259.1|FL043259
EST:     ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
EST: gi|211091949|gb|FL022375.1|FL022375
EST:     ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattc ... ctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag

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