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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgctaacctttaaatctgagcagtagcattattcccatttcttagtactatatctggatttggctttcagtttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC

Basic information

species Zea mays
transcript GRMZM2G069970_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069970_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 3
gtaacttgctaacctttaaatctgagcagtagcattattcccatttcttagtactatatctggatttggctttcagtttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatt-tagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC
| | | | || |||| | | | || | | ||| || || || || || || | ||| || | ||||||| |||||||| |||| ||||||||||||||| |||||| | || ||||||||||| |||||||| || |||||||||||||||||||| ||||| |||||||| ||||| ||||||||
------------------------gtaattgatactgacagtatgcactagtgttgt-tttgcact--acttccatactgtgttttag-agcaattccatgaccatttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC

upper sequence: GRMZM2G069970_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g50380.3 (Oryza sativa), 3'ss of exon 2
gtaacttgctaacctttaaatctgagcagtagcattattcccatttcttagtactatatctggatttggctttcagtttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatt-tagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC-----------------
| | | | || |||| | | | || | | ||| || || || || || || | ||| || | ||||||| |||||||| |||| ||||||||||||||| |||||| | || ||||||||||| |||||||| || |||||||||||||||||||| ||||| |||||||| ||||| ||||||||
------------------------gtaattgatactgacagtatgcactagtgttgt-tttgcact--acttccatactgtgttttag-agcaattccatgaccatttcattcttccatggcttatattgcagggtttgcatctgaacagAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCCTGTGAAGCCTCAAATAG
















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|5928871|gb|AW056163.1|AW056163
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
EST: gi|78086197|gb|DV514590.1|DV514590
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
EST: gi|211178849|gb|FL219806.1|FL219806
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGNAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
EST: gi|148970773|gb|EE021521.2|EE021521
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
EST: gi|149085363|gb|EE174870.2|EE174870
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
EST: gi|93283061|gb|EB675325.1|EB675325
EST:     TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAA                         GGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT
genomic: TCCAGAGACGGCCTGCTATATCAATGATCATCTCTTCCAGAATCTGAAAAgtaacttgct ... ttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC
                                             ttgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgctaacctttaaatctgagcagtagcattattcccatttcttagtactatatctggatttggctttcagtttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatttagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA