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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattatcgttttatcatgggtgtgattctgtttgtaagcaaagtattaattcccggtacccttaaaaaacgatttgttcttgatataaggaagtgatatctgttaattgagatgtttccatcatcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGTTCCATTTCTCCCCTCTATATGGGCAGTCAAATGTGTTGATCTACACTGC

Basic information

species Oryza sativa
transcript LOC_Os05g43790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 4
gtgagaattatcgttttatcatgggtgtgattctgtttgtaagcaaagt-attaattcccggtacccttaaaaaacgatttgttcttgatata-aggaagtg--atatc-tgttaattgagatgtttc--catcatcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGTTCCATTTCTCCCCTCTATATGGGCAGTCAAATGTGTTGATCTACACTGC
                                      ||||| |   | ||   |          |||  | |     | | ||||||| |  ||||||||  ||||| ||   | |||||| | |    ||  ||| |||||||||||||| |||||||||| |||||||| ||| | || || || || |||||| ||||||||||||| ||||||||||| ||||||||||||||||||||
--------------------------------------gtaaggactatcatcggtgtgattctgtcttgtagagttgctagctcttgatttgtaggaagtggaatatcatgactaatgagatatcttggtattttcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC
















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|218503663|gb|FG954349.1|FG954349
EST:     CTGGAACATGGCGATACAGCCTG                         CTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGT
genomic: CTGGAACATGGCGATACAGCCTGgtgagaatta ... tcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGT
EST: gi|33662767|gb|CF293734.1|CF293734
EST:     GCAAGAGATTACTTCAGTTAGAGAAATCTGGAACATGGCGATACAGCCTG                         CTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGT
genomic: GCAAGAGATTACTTCAGTTAGAGAAATCTGGAACATGGCGATACAGCCTGgtgagaatta ... tcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatataaggaagtgatatctgttaattgagatgtttccatcatcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGTTCCATTTCTCCCCTCTATATGGGCAGTCAAATGTGTTGATCTACACTGC
                      tgttaat  putative branch site (score: 3)
                                    tttccatcatccttt  putative PPT
                      tgttaatt  TA-rich tract