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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgttactgcacatgaggtgtgtaggtggctgtatttctcttaatcaaaaagttatttaccatccgtaaagtaatagattctgatctattttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTA

Basic information

species Zea mays
transcript GRMZM2G095323_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 5
tttatgttactgcacatgaggtgtgtaggtggctgtatttctcttaatcaaaaagttatttaccatccgtaaagtaatagattctgat-ctattttctt-agAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTA
|  || |    |  || ||  |   | | |   | ||||| | ||  |  |  | | |||  |||| | || |      |||| | |  |||| | ||| ||||| ||||||||||| |||| |||||||| || ||||| || |||||||||||| || |||| || |||||||| |||||||||| |||| |||||||| 
tgcatctcctagtgca-gatctaacttgtttaatctatttttgtttcttcatta-tgattggccatgcttagaaatgctgattgttacactatctcctttagAGTCAAGGAAGATGCTTGGCTGATCTATGTGGAGCACTTCACTGTGATCTGATGTTGGAGTTTAAGAAACCAAAGAGTAAATGCAGTGCAACTGCAGCTG
















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|91878948|gb|EB408905.1|EB408905
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCCCAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATG
EST: gi|78125182|gb|DV543566.1|DV543566
EST:     AGTTCATTGATCAGCATTTTGAATATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCGTGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|148956175|gb|EC901959.2|EC901959
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|71770155|gb|DR968092.1|DR968092
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|76293362|gb|DV032930.1|DV032930
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|71439253|gb|DR820303.1|DR820303
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|71310796|gb|DR791700.1|DR791700
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|88755486|gb|DY539627.1|DY539627
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|71773093|gb|DR971011.1|DR971011
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|74233328|gb|DT641242.1|DT641242
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|78116974|gb|DV535361.1|DV535361
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|78115630|gb|DV534018.1|DV534018
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
EST: gi|71428073|gb|DR809123.1|DR809123
EST:     AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAAT                         AGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG
genomic: AGTTCATTGATCAGCATTTTGAAAATCGCCACAAGAATCTTGTGGATAATgtatgcttac ... attttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaaaaagttatttaccatccgtaaagtaatagattctgatctattttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTA
                                    ttctgat  putative branch site (score: 3)
                                          tctattttctt  CT-rich tract
                        taaagtaatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgttactgcacatgaggtgtgtaggtggctgtatttctcttaatcaaaaagttatttaccatccgtaaagtaatagattctgatctattttcttagAGTGAAGGAAGATGCATGGCAGATCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT