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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattagcatcattagatcctaatgtctcaatcagagctaaattttgcaacacatgttccatgaactgctaaagctaacgggtaatacatcttgtttatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGTGCATCTGGTGGGATAATGCTTCTTGGAATAGTCGGATTTTGTATATTAT

Basic information

species Zea mays
transcript GRMZM2G007871_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 5
gtaatattagcatcattagatcctaatgtctcaatcagagctaaattt-tgcaacacatgttccatgaactgctaaagctaacgggtaatacatcttgtttatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGTGCATCTGGTGGGATAATGCTTCTTGGAATAGTCGGATTTTGTATATTAT
|||||||   ||||  |   || | |      | | | | |||||  | | ||    ||||| ||||   || |  ||  ||    ||| ||    ||||| || | |||||| |||||||||||||||||||||||||||| ||  | ||||| ||||||||||||||||| |||||||||||||||||||| ||  | || ||| | |
gtaatatggacatctgttattcttgacactctacttaaaactaaacatatacatgtgatgtttcatgg--tgttcgagacaaacattaacacggtgtgtttgtggtccagGGGATGCAAATGGGCATTGCTTTGCCCAAGTTCTTGTTGAATATGGATGGTGCATCTGGTGGAATAATGCTTCTTGGAATAGTAGGGCTATGCATACTCT
















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|71436007|gb|DR817057.1|DR817057
EST:     CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|32838158|gb|CD977836.1|CD977836
EST:     CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|22935564|gb|BU571839.1|BU571839
EST:     TATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAA-GGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: TATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|32837602|gb|CD977280.1|CD977280
EST:     CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: CTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|87156492|gb|DY401281.1|DY401281
EST:     AATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: AATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|87157186|gb|DY401975.1|DY401975
EST:     ATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: ATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
EST: gi|87157024|gb|DY401813.1|DY401813
EST:     AATATGGTCACCCTGATGGGCGGCAG                         GGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT
genomic: AATATGGTCACCCTGATGGGCGGCAGgtaatattag ... tatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttccatgaactgctaaagctaacgggtaatacatcttgtttatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGTGCATCTGGTGGGATAATGCTTCTTGGAATAGTCGGATTTTGTATATTAT
                     agctaac  putative branch site (score: 2)
                                      tcttgttt  putative PPT
                                           tttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattagcatcattagatcctaatgtctcaatcagagctaaattttgcaacacatgttccatgaactgctaaagctaacgggtaatacatcttgtttatgattcagGGGCTGCAAATGGGCATTGCTTTGCCCAAGTTTTTACTAAATATTGATGGTGCATCTGGTGGGATAATGCTTCTTGGAATAGTCGGATTTTGTATATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG