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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccaatatttttttttcgagaaaattcgtttgtttccttggtctaatggccctttcatacaattctgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTCTTGCCTGGAGGGTAAAAGAACTGAACTTGTTGAGCATGTTCTTAATGAC

Basic information

species Oryza sativa
transcript LOC_Os01g40340.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 3
gtaagtcca-atatttttttttcgagaaaattcgtttgtttccttggtctaatggccctttcatacaattct-gaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTCTTGCCTGGAGGGTAAAAGAACTGAACTTGTTGAGCATGTTCTTAATGAC
||| ||    |||| ||||||| |    || || | ||||||   |||| || | |||  |  ||   || | | |   |||||| ||||||||||| |||||||||||||||||||||||||| |||||  |||||||||||||||||||| ||||| ||||||||||||||||| |||| 
gtatgtgtggatatgttttttttgg---aactcttctgtttctccggtcaaaagccccccttttatgttttttgtaacacagGTATCCATATAACAACTTTTTGCACCATCATGTTGAGAATATAATTGTTGCTTGCCTGGAGGGTAAAAGACCTGAAGTTGTTGAGCATGTTCTTCATGAA
















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|29680806|gb|CB677081.1|CB677081
EST:     GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
EST: gi|29612947|gb|CB617960.1|CB617960
EST:     GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
EST: gi|88717309|gb|CI740819.1|CI740819
EST:     TGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: TGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
EST: gi|58672704|gb|CK061390.1|CK061390
EST:     GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
EST: gi|88417264|gb|CI576338.1|CI576338
EST:     GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
EST: gi|58689270|gb|CK077957.1|CK077957
EST:     GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGA                         GTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC
genomic: GAGCTTATCAGGCAATCGGCAATAAAGCGATCTGTTGATTTATTCTTCGAgtaagtccaa ... tgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattcgtttgtttccttggtctaatggccctttcatacaattctgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTCTTGCCTGGAGGGTAAAAGAACTGAACTTGTTGAGCATGTTCTTAATGAC
                    gtctaat  putative branch site (score: 3)
                                    atacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccaatatttttttttcgagaaaattcgtttgtttccttggtctaatggccctttcatacaattctgaactgcagGTACCCATATAACAATTTTTTGCACCATCATGTTGAGAATATTATTGTCTCTTGCCTGGAGGGTAAAAGAACTGAACTTGTTGAGCATGTTCTTAATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC