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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 5
gtatgtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcg-tctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC
            | || | |||    ||| |  |     || ||  |  |   | ||| |||   | ||  |   |||       |||||  ||   || |||| ||| |  ||| ||||||| |||||||||||||||||||||||||| |||  ||||||||||||| || | || |||||  |||| || || || ||| | || || ||||||||||
-----------ctctatctatttgtttattttgtgatttctgctcctt-gcctccttctagagatttcacatacgtaa------aaaacatcca---taatgttgtctacaatctttgcagATCCGAAATGAGAAGGCCAGGAGATACTTAAGCTGCATGCGGAAAAAATATCCCGTGCCCTTTACTCATAAATTTCGAAATGCCGATCCTTTGGCTCTTC

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 5
gtatgtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcg-tctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC
                       |||     | || |      ||||  || |  |         || |    |   | | |  || | ||   || || |||| ||| || ||| ||||||||||||||||||||||||||||||| ||||||  ||||||||||||| || | || |||||  |||| || || ||  || |||| || ||||||||||
--------------------ccttcaggccccatttatttgtttattttgtgatgtctgctcct-tctagagattccacatgcggagaaaacatccataatgttgtctacggtctttgcagATTCGAAATGAGAAGGCCAGGAGATATTTGAGCTGCATGCGGAAAAAATATCCCGTGCCCTTTACTCATAAATTTCGACATGCTGATCCTTTGGCTCTTC
















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|33795692|gb|CF323716.1|CF323716
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAG
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAG
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCG
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCG
EST: gi|33381883|gb|CF197226.1|CF197226
EST:     TTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: TTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGACGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCA
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCA
EST: gi|58589575|gb|CF987883.1|CF987883
EST:     TATTATAACAGATCTTCTTGGAACTCCATCGATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: TATTATAACAGATCTTCTTGGAACTCCATC-ATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGGCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC
                            accttac  putative branch site (score: 3)
                                     ttttctgcgtctct  putative PPT
          taataagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT