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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgacgaatagttctattttatactgtataatacgaacatttgtattttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA

Basic information

species Zea mays
transcript GRMZM2G090087_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 7
--------catgacga-atagttctattttatactgtataatacgaacatttgtattttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA
          | || |  |||||  || ||   |  | || |  |   ||      ||||| ||     | |||  |  |   |  | ||| || || | | ||  |||||||||||||||||||| |||||||| || |||||||| || ||||| ||| | ||||||||||| || |||||||||||||| || ||||| |||||||
gtgagtactctaacaatgtagttgaatgtttagccatttatttaggcaataccaggttttttttgggtatcatgttagctctaatgttatatatata-attctgaacagGTTGCAATTATCACACCGTTCAATTTCCCATTGGAGATTCCATTACTGCAACTAATGGGAGCACTGTATATGGGAAATAAACCTGTCCTCAAAGTTGACA

upper sequence: GRMZM2G090087_T02 (Zea mays), 3'ss of exon 7
lower sequence: EFJ08918 (Selaginella moellendorffii), 3'ss of exon 6
catgacgaatagttctattttatactgtataatacgaacatttgtattttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA
                                        |  || | |    ||| | ||| ||        ||  | | |     || ||  || ||||| || || |||||||||||||||||||| |||||||| ||  | || ||  | ||||| ||||| |||||||| |||||  |  |  | || ||||| |
---------------------------------------gtaagtgtctcg-gttctagtttctg--------gatttgaca-----agcatgcgtccagGTCGCTATCATCACACCATTCAATTTTCCTTTGGAGATACCGGTGCTCCAGCTTATGGGGGCACTCTACATGGGCAATAAGGCTCTGGTGAAAGTTGATA

upper sequence: GRMZM2G090087_T02 (Zea mays), 3'ss of exon 7
lower sequence: EFJ29772 (Selaginella moellendorffii), 3'ss of exon 6
catgacgaatagttctattttatactgtataatacgaacatttgtattttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA
                                        |  || | |    ||| | ||| ||        ||  | | |     || ||  || ||||| || || |||||||||||||||||||| |||||||| ||  | || ||  | ||||| ||||| |||||||| |||||  |  |  | || ||||| |
---------------------------------------gtaagtgtctcg-gttctagtttctg--------gatttgaca-----agcatgcgtccagGTCGCTATCATCACACCATTCAATTTTCCCTTGGAGATACCGGTGCTCCAGCTTATGGGGGCACTCTACATGGGCAATAAGGCTCTGGTGAAAGTTGATA

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|60339011|gb|DN205984.1|DN205984
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|67026280|gb|CO455029.1|CO455029
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTACAATTATCACACCATTCAA-TTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|211228711|gb|FL216929.1|FL216929
EST:     STAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|211228709|gb|FL216927.1|FL216927
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
EST: gi|211097512|gb|FL395914.1|FL395914
EST:     GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCA                         GTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA
genomic: GTAACCATCTTGGACAAAGAAGTAATGGCTACCGTTGGCCATATGGCCCAgtaagtgttc ... atttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA
                             agctaat  putative branch site (score: 3)
     ttattcaaatttatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgacgaatagttctattttatactgtataatacgaacatttgtattttttattcaaatttatgacatgttagagctaatagatctagaatttgtgcagGTTGCAATTATCACACCATTCAATTTTCCGTTGGAGATCCCCTTACTACAATTGATGGGAGCACTATACATGGGAAATAAACCAGTACTCAAGGTTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA