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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaataaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC

Basic information

species Zea mays
transcript GRMZM2G137468_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g30900.1 (Oryza sativa), 3'ss of exon 3
gtaa-ataaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtct-ctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
 ||   |     | ||| || |  ||   ||    |  |  || |   | ||        | ||   | || |  |    ||||| |||  |  || | ||||| |||||| |||||| || || ||||| |||||||| |||||||||||||| || |||||||| || ||||| |||||||| || |||||||| |||||
-tattgtgtgagtctaatatgtgattttgaattaagtgtcgatataaatatgtatgaataatgaccgtactaaacttcaataaattgttt-atgtggtatagATCTACCTCCTGATAAGGAAGCATTGGATTGGAACACAAGGATGAAAATTGCGGCTGGTGCTGCTAAGGGACTAGAGTACCTTCATGACAAAGCAAATCC

upper sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
----------gtaaa-taaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
          ||| | |  | ||| |  ||   |||  | | | |||| | ||  || |   | ||   |   | ||  | ||||     || |||          || |||| | || |  || || ||  | || || |||||||||||||||||||| || || || || || |||||| |||| ||||| ||||||||||| || ||
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatca-ttattta--tgaactgg--------agtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC

upper sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G44580.2 (Glycine max), 3'ss of exon 3
gtaaataaatatataagatattcttccaaacagtgcattcatt-ttgttttgatctgtcgagga-gtctctcatttgacctaaatggttccacttgatg-tagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
   || |  | |    | |||| |  |   |     ||   |   |  | |    ||  ||  |   ||    ||| | |   ||   |  ||| || |  |||| | || |  ||||| ||  | || || |||||||||||||||||||| || || || || || |||||| |||| ||||| || |||||||| |||||
---aaaatgtttccttgttattatatctgtcttcttatgattgactagtatctcatgctgataataactaatgtttaatcattatttatggactggagggcagATCTTCCCCCGGATAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCATGACAAAGCAAATCC

upper sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttg-atgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
                                          ||||| |  ||   |  ||  || ||     | ||  || ||  |   |||   || |||  | ||   ||| || ||  | |||| ||||||||| ||||||||||| || || || |||||||  ||||||||||||||||| |||||||| |||||
-----------------------------------------gtttgtct--attaatttagttgtttcctgcat-acgaaactgagtgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTACATGACAAAGCAAATCC

upper sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttg-atgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
                                          ||||| |  ||   |  ||  || ||  |  | ||  || ||  |   |||   || |||  | ||   ||| || ||  | |||| ||||||||| ||||||||||| || || || |||||||  |||||||||||||| || |||||||| |||||
-----------------------------------------gtttgtct--attaatttagttgtttcctacat-acgaaactgagtgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTGCATGACAAAGCAAATCC

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|211477955|gb|FL115135.1|FL115135
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|26558503|gb|CA830738.1|CA830738
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|87156740|gb|DY401529.1|DY401529
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
EST: gi|22472491|gb|BU036971.1|BU036971
EST:     TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACG                         ATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG
genomic: TCTTGTTTATGAATATATGCCCTCTGGATCACTTGAAGATCATTTGCACGgtacaaatgc ... cttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgatctgtcgaggagtctctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
                                        ttccactt  CT-rich tract
                                 taaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC