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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG

Basic information

species Zea mays
transcript GRMZM2G171406_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g43594.3 (Oryza sativa), 3'ss of exon 6
gtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtactt--ttcagATGCTGAAGAATGCAAGCCTTGAAGAG
        |||  ||  ||        ||||  | |||||||    | || |  ||  ||  || | ||             || | | ||   | |||||   | ||||||||||||||||||||| ||||||||
--------gtgagagtact--------atgttggaaacttgtatgacgctgaccaaacttatgt-gcaa--------aggactcatgttttgcactgtactacatgcagATGCTGAAGAATGCAAGCATTGAAGAG

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 6
gtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtactt--ttcagATGCTGAAGAATGCAAGCCTTGAAGAG-------------------------------------------------------------------------
        |||  ||  ||        ||||  | |||||||    | || |  ||  ||  || | ||             || | | ||   | |||||   | ||||||||||||||||||||| ||||||||                                                                         
--------gtgagagtact--------atgttggaaacttgtatgacgctgaccaaacttatgt-gcaa--------aggactcatgttttgcactgtactacatgcagATGCTGAAGAATGCAAGCATTGAAGAGGTAATGCAACTGATCCTAAAGGCATCTCTCATTTTATCAGGGAACTACACCTAAATAATATCACAATAAATAT
















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|71429669|gb|DR810719.1|DR810719
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|94475041|gb|EB703999.1|EB703999
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|16919153|gb|BM074062.1|BM074062
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|93012917|gb|EB638437.1|EB638437
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|60397188|gb|DN230004.1|DN230004
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|94475040|gb|EB703998.1|EB703998
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|89250482|gb|DY622268.1|DY622268
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|5069938|gb|AI737903.1|AI737903
EST:     AGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: AGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|89251407|gb|DY623193.1|DY623193
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattttcagttgtaactcttactgttgatcgtatctttggccgtacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
                                             tacttttc  CT-rich tract
                                 tatcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA