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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA

Basic information

species Zea mays
transcript GRMZM2G024668_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ22362 (Selaginella moellendorffii), 3'ss of exon 3
aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA
                                       | | || |   ||    ||| |      | |     | || | || || || ||   |||| | || || ||||| ||| |   ||| |||||||| |||||||||||||| || || |||||||| || |||||  |||||||||||||||| ||||| |
---------------------------------------gtaggcgtttctatttcatcgatgtgaaacaagtagttac-tctgattttggttggcacagCTTGAATACCTTGAAGAGAGGAAGCTCAAGGATCTCATCAAGAAGCACTCCGAATTTATCAGCTATCCCATCTCCGTCTGGATCGAGAAGACTACTGACA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ25533 (Selaginella moellendorffii), 3'ss of exon 3
aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatac-tacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA
                                       | |||| |   ||    ||| |      | |  ||||||   |||| || || ||   |||| | ||||| ||||| ||| |   ||| |||||||| |||||||||||||| ||||| |||||||| || |||||  |||||||||||||||| ||||| |
---------------------------------------gtatgcgtttctatttcatcgatgtgaaacaagtacttac--tttgattttggttggcacagCTTGAGTACCTTGAAGAGAGGAAGCTCAAGGATCTCATCAAGAAGCACTCCGAGTTTATCAGCTATCCCATCTCCGTCTGGATCGAGAAGACTACTGACA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 3
aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA
                            ||   |||||||  |      || ||      |   ||  |   ||| ||| ||| | |     | |  ||| | || || || |||||| |  |||| ||||||||||||||||||||||| |||||||||||||| || |||||  ||||| | |||||||| || ||||
---------------------------gtgtgtttttgtgtttttgctgtttgag-----actatccctgtgactaaactttttcatac---tgcgccagCTTGAATACCTCGAGGAGAGGAGGCTCAAGGATCTGATCAAGAAGCACTCCGAGTTCATCAGCTATCCCATCTCCGTCTGGGTTGAGAAGACGACCGAGA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 3
aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA
                            ||   |||||||  |      || ||   |  |   ||  |   ||| ||| ||| | |     | |  ||| | || ||||| |||||| |  |||| ||||||||||||||||||||||| |||||||||||||| || |||||  ||||| | || ||||| || ||||
---------------------------gtgtgtttttgtgtttttgctgtttgagacttta---tccctgtgactaaactttttcatac---tgcgccagCTTGAATATCTCGAGGAGAGGAGGCTCAAGGATCTGATCAAGAAGCACTCCGAGTTCATCAGCTATCCCATCTCCGTCTGGGTTGAAAAGACGACCGAGA

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|22521360|gb|BU080171.1|BU080171
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
EST: gi|20208342|gb|BQ134431.1|BQ134431
EST:     GCAACTTGAGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: GCAACTTG-GCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
EST: gi|18648849|gb|BM497668.1|BM497668
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
EST: gi|4776637|gb|AI665640.1|AI665640
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
EST: gi|211138726|gb|FL294024.1|FL294024
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAGGGATGATCAG                         TTAGAGTATCTTGAGGGAGCGCCG-CTGGAGGATCTGATCAAGAGGCACTT
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGG-AGCGCCGGCTGAAGGATCTGATCAAGAAGCACT-
EST: gi|21843518|gb|BQ704099.1|BQ704099
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCG
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCG
EST: gi|21843415|gb|BQ703996.1|BQ703996
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
EST: gi|22715674|gb|BU197898.1|BU197898
EST:     AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAG                         TTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA
genomic: AGCAACTTGGCAGGGGTACAAAGATGACCCTTTACCTCAAGGATGATCAGgtatatcaca ... ttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA
                           acttaac  putative branch site (score: 3)
                                           tgttttct  putative PPT
        aatatcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatagatgtacatgtttgcaatggccctgaaattttgtgaatgcatcattagaatatcaaaagtctatactacttaacatttgcttgtgttttctacagTTAGAGTATCTTGAGGAGCGCCGGCTGAAGGATCTGATCAAGAAGCACTCAGAGTTCATCAGCTACCCAATCTCTCTCTGGATCGAGAAGACCACTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - -gatgtac
- - - - - - -tgtttgc
- - - - - - - - - - - - -ccctgaa
- - - - - - - - - - - - - - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaa