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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCGTCGAGCTCCACATGGTCCACGCCAGCGACGACGGCAACGTCACCGTGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatctaccatatgcattaatgcatcctcgtcgtcgtcgtcgttggcggcatagcatcttcgacgatagtaaccgccgactctgcgtttaaacttggtctgttcgcggacgacgcgcggcggcacag

Basic information

species Zea mays
transcript GRMZM5G807267_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807267_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g33660.1 (Oryza sativa), 5'ss of exon 4
CCCCGTCGAGCTCCACATGGTCCACGCCAGCGACGACGGCAACGTCACCGTGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatcta--ccatatg-cattaatgcatcctcgtcgtcgtcgtcgttggcggcatagcatcttcgacgatagtaacc--gccgactctgcgtttaa-acttggtctgttcgcggacgacgcgcggcggcacag
|||  | |||||||||||||| ||| ||| |||  | |||||| |||||||  ||||| | |||||||| ||||||||||| || || ||  ||   ||||||    | |     |||||| | |   ||||   |   |       |   |  ||    |      |     |||| | |    |   |||||    | | |  |||| | || ||     | |   |   |     
CCCACTGGAGCTCCACATGGTTCACACCAACGAAAATGGCAACATCACCGTTCTGGCCTTTCTCTACCGATTTGGCAGGCCAGACCCGTTCTTCGAACAGgtagatcacccgattcatatgacgtggctgcacggtgcacactacgatt-ctaccgttcaaaggcaataatttatagcagcatgtcttcctctgttcctgatatgtggtgt-tttgcccttcatggatgatag-----
















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|89758326|gb|DY687544.1|DY687544
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|60344770|gb|DN211743.1|DN211743
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|148933555|gb|EC877415.2|EC877415
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGG
EST: gi|74244873|gb|DT652787.1|DT652787
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|76288688|gb|DV028256.1|DV028256
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|86469687|gb|DY236057.1|DY236057
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|50324602|gb|CO519728.1|CO519728
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|86474309|gb|DY240679.1|DY240679
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|211385816|gb|FL436939.1|FL436939
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGTTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|74239798|gb|DT647712.1|DT647712
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGTTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|60346845|gb|DN213818.1|DN213818
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|76014111|gb|DT941281.1|DT941281
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|71417345|gb|DR804018.1|DR804018
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACTAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGATCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|149095902|gb|EE181563.2|EE181563
EST:     TGGGGGCCATGCTTTCCCGGTTGGGCAGGCCGGATCCTTTGCTTTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|91050066|gb|EB160484.1|EB160484
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|211295581|gb|FL447840.1|FL447840
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|89248779|gb|DY620565.1|DY620565
EST:     GCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: GCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|74239799|gb|DT647713.1|DT647713
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
EST: gi|71316204|gb|DR794778.1|DR794778
EST:     TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAG                         ATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG
genomic: TGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatc ... ggcggcacagATCCAGGACAAGCTGGCCGCGCTGCACGCGGAGGGCTGCAGAGCGGACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCGTCGAGCTCCACATGGTCCACGCCAGCGACGACGGCAACGTCACCGTGGTGGCCATGCTCTACCGGTTTGGCAGGCCGGATCCTTTGCTCTGGCAGgtactgaatctaccatatgcattaatgcatcctcgtcgtcgtcgtcgttggcggcatagcatcttcgacgatagtaaccgccgactctgcgtttaaacttggtctgttcgcggacgacgcgcggcggcacag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG