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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgaagttttttttcttcttgttaaaataggttttggtgcactcatgaattcatgaagtgtgatcgttttctattgccgttgccacccttgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCGGTGGTTGCGGTGATGAACGTATTTTGGTTCTGGAAGATACTCAAGGGGA

Basic information

species Zea mays
transcript GRMZM2G021589_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021589_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g60120.2 (Oryza sativa), 3'ss of exon 8
------------------------------------------------catgaagttttttttcttcttgttaaaataggttttggtgcactcatga-attcatgaagtgtgatcgttttctat-tgccgttgccacccttgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCGGTGGTTGCGGTGATGAACGTATTTTGGTTCTGGAAGATACTCAAGGGGA
                                                 || || ||  | | | | |   |   |  ||   |  |   ||  | | |||  ||   |   |  | | ||| |  ||   |||||  |||      |||| ||  |||||||||  | | || ||||||||  |  || | |||||  ||| | | || ||||||||| |||||||||||||||||||| ||||||| |
gtatgcatgactttaccaggtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatatttttcttgttacatttctg---ttctaatgctctctgtacgcatatgccatactt-----tcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCGGCGCTGGCAGTGATGAACCTATTTTGGTTCTGGAAGATATTCAAGGGAA
















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|22520700|gb|BU079511.1|BU079511
EST:     TAATCTTATTCATATATATGTTCCCCCATATGTATTTTCATCTTGATCAG                         GCGAGATCCATCTTCAGCTTAGGGTTTTACAGCTTGGTGGCAGTGCCGTCG
genomic: TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggtat ... tgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
EST: gi|32944348|gb|CF049167.1|CF049167
EST:     TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAG                         GCGAGATCCATCTTCAGCTTAGGCTTCTACAGCTTGGTGGCAGTGCCGTCG
genomic: TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggtat ... tgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
EST: gi|13557777|gb|BG549133.1|BG549133
EST:     TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAG                         GCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
genomic: TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggtat ... tgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
EST: gi|10450892|gb|BE924816.1|BE924816
EST:     TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAG                         GCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
genomic: TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggtat ... tgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG
EST: gi|16380079|gb|BI993301.1|BI993301
EST:     TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAG                         GCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGACAGTGCCGTCG
genomic: TAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggtat ... tgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaattcatgaagtgtgatcgttttctattgccgttgccacccttgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCGGTGGTTGCGGTGATGAACGTATTTTGGTTCTGGAAGATACTCAAGGGGA
                                      ccacccttgtttccc  CT-rich tract
                      ttttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgaagttttttttcttcttgttaaaataggttttggtgcactcatgaattcatgaagtgtgatcgttttctattgccgttgccacccttgtttcccagGCGAGATCCATCTTCAGCTTAGGGTTCTACAGCTTGGTGGCAGTGCCGTCGGTGGTTGCGGTGATGAACGTATTTTGGTTCTGGAAGATACTCAAGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA