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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcactgatatcatgaatagcttctttgcatttagatttcgtaacacgttgaattttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTAAATAACGCCATTTCAGAGAATGAAACTTCGAAGAACAACAAACCAGGAA

Basic information

species Oryza sativa
transcript LOC_Os02g38840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 4
gtaagtcactgatatcatgaatagcttctttgcatttagatttcgtaacacgt---------tgaattttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTAAATAACGCCATTTCAGAGAATGAAACTTCGAAGAACAACAAACCAGGAA
||||||   | ||||  || |||||| ||      | | |  || | ||   |         ||||   |   | ||| | |||||||||||||| |||||  |||| | |||||||||||  | ||||||||| || || || ||| |||||||||| || |||||  |  | ||||
gtaagtttttaatattgtgtatagctcctgaaatctgaaaactcttgacgtctgtaatcatgtgaaaaattcgtacagGTAAAATATGTTAGTGGCTCCTATGATAGGGTGGAAGGATTTGAGTTATTAAATAAGGCAATCTCTGAGTATGAAACTTCAAAAAACAATGACTCGGGAA
















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|25798694|gb|CA754655.1|CA754655
EST:     ATACCTCACAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA                         ATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTA
genomic: ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTAgtaagtcact ... ttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTA
EST: gi|88304205|gb|CI599893.1|CI599893
EST:     ATAC-TCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA                         ATTAAATATTTTAGTGGTTCCTACA-TAGCGGGGAGGGTTTTG-ATTATTA
genomic: ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTAgtaagtcact ... ttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTA
EST: gi|29635730|gb|CB640739.1|CB640739
EST:     ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA                         ATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAAGATTTGCATCA
genomic: ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTAgtaagtcact ... ttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCA
EST: gi|29616736|gb|CB621748.1|CB621748
EST:     ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA                         ATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGAATCATTA
genomic: ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTAgtaagtcact ... ttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTA
EST: gi|88445341|gb|CI587235.1|CI587235
EST:     ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCA-TTA                         ATTAA-TATGTTAGTGGTTC-TACA-TAGCGGG-AAG-ATTTGC-TCAT
genomic: ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTAgtaagtcact ... ttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaatagcttctttgcatttagatttcgtaacacgttgaattttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTAAATAACGCCATTTCAGAGAATGAAACTTCGAAGAACAACAAACCAGGAA
                            tcgtaac  putative branch site (score: 2)
                                           ttttctttgc  putative PPT
                   atttagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcactgatatcatgaatagcttctttgcatttagatttcgtaacacgttgaattttctttgcagATTAAATATGTTAGTGGTTCCTACAATAGCGGGGAAGGATTTGCATCATTAAATAACGCCATTTCAGAGAATGAAACTTCGAAGAACAACAAACCAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC