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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaaaagaagtgagcatttatctgatcctgtaaggcttcagtttcttgttaactttataactcttgtattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT

Basic information

species Zea mays
transcript GRMZM2G144362_T06
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g41390.4 (Oryza sativa), 3'ss of exon 3
gtaagtgaaaaag-aagtgagcatttat-ctgatcctgtaaggcttc-agtttcttgttaactttataactcttg--tattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
||||||||||||| |||||||||||||  |||| ||||||||||||   |||||||||  | ||||  ||||||   ||| || |  || |  |||             ||| |   |||       | | |  || | | |||||||||  ||||||| ||||| || ||| ||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||| ||||||
gtaagtgaaaaaggaagtgagcatttaagctgaacctgtaaggcttttggtttcttgtgtaatttagtactcttatttatcttttccatcacttga-------------tgatacctctttctggtattcttaactaatttcagGACCTCCATTAGCCACATGGACTTCCCAAAAATTGTGGAGGGAGGGCTCAAACAGATGTTAGAATTACTTGGTGATGACAATGCACCGTTTGAT

upper sequence: GRMZM2G144362_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g41390.3 (Oryza sativa), 3'ss of exon 3
gtaagtgaaaaagaagtgagcatttatctgatcctgtaaggcttc-agtttcttgttaactttataactcttgt--attttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
                                   |||||||||   |||||||||  | ||||  |||||| |  || || |  || |  |||             ||| |   |||       | | |  || | | |||||||||  ||||||| ||||| || ||| ||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||| ||||||
-----------------------------------gtaaggcttttggtttcttgtgtaatttagtactcttatttatcttttccatcacttga-------------tgatacctctttctggtattcttaactaatttcagGACCTCCATTAGCCACATGGACTTCCCAAAAATTGTGGAGGGAGGGCTCAAACAGATGTTAGAATTACTTGGTGATGACAATGCACCGTTTGAT
















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|76291844|gb|DV031412.1|DV031412
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|94474973|gb|EB703931.1|EB703931
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|76286746|gb|DV026314.1|DV026314
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|71441108|gb|DR822158.1|DR822158
EST:     GAGGTTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|78088519|gb|DV516912.1|DV516912
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|78079635|gb|DV508047.1|DV508047
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|148933496|gb|EC877205.2|EC877205
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|148981958|gb|EE028016.2|EE028016
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|91055958|gb|EB166376.1|EB166376
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|89249445|gb|DY621231.1|DY621231
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|94479450|gb|EB708408.1|EB708408
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACCAGACTGGAAT                         GACCCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACC-TCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCA
EST: gi|148985933|gb|EE029846.2|EE029846
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACCAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|149014216|gb|EE043770.2|EE043770
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|71430541|gb|DR811591.1|DR811591
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|93282998|gb|EB675262.1|EB675262
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|76937601|gb|DV175194.1|DV175194
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|93281830|gb|EB674094.1|EB674094
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|71332805|gb|DR803405.1|DR803405
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|50333623|gb|CO528749.1|CO528749
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|78123131|gb|DV541515.1|DV541515
EST:     GAGGCTACTACGTGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|94477309|gb|EB706267.1|EB706267
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|76010683|gb|DT937853.1|DT937853
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|71449941|gb|DR830991.1|DR830991
EST:     GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: GAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAATgtaagtgaaa ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
                                           tgcttac  putative branch site (score: 2)
                                             cttactcc  CT-rich tract
      agattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaaaagaagtgagcatttatctgatcctgtaaggcttcagtttcttgttaactttataactcttgtattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG