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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattttcttattcttgactaagcttgtagtctgtatcttgtgcatcgtgtaagtcgttttctttaactttacatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT

Basic information

species Oryza sativa
transcript LOC_Os08g32850.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 5
gtaagtattttctt----attcttgactaa-gcttgtagtctgtatcttgtgcatcgtgtaagtcgttttctttaactttacatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT
||||| ||||| ||    |  ||   ||     ||| | | ||  |||| ||||| ||| || ||  ||| |||  ||||| ||||||||||||||| |||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||||||||| |||||  | ||||| |||||||
gtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT

upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G14860.1 (Glycine max), 3'ss of exon 4
gtaagtattttcttattcttgactaagcttgtagtctgtatcttgtgcatcgt-gtaagtc-------gttttctttaacttt-------acatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT
  ||   || |   | || |   ||  |  |||| ||| |      ||   || | || ||       ||||  | |||| ||       |  ||| |||||||||| ||||| || ||||| || |||| ||||||||| ||||||||||||||||||||||| ||||| || |  ||||| || || || ||  |||| |
--aaaatttctacaactcatctatataccagtagcctggaagaaaagcgcagttgcaattccctatctgtttattataaccttttttgaaatctttttgcagACACTTGTGACAGGATTTGCTAGAATTTTTGGACAGCCTGTTGGAATTATTGGAAACAATGGGATTTTATTCAATGAATCTGCACTGAAAGGGGCCCATT

upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G33620.1 (Glycine max), 3'ss of exon 4
gtaagtattttcttattcttgactaagcttgtagtctgtatcttgtgcatcgt-gtaagtc------gttttctttaacttt------acatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT
 |||   || |   | || | | ||  || |||| ||| |      ||   || | || ||      ||||  | |||| ||      |  ||| |||||||||| ||||| || ||||| || ||||  |||||||| ||||||||||||||||||||||| ||||| || |  ||||| || || || ||  |||| |
ataaaatttctacaactcatcagtatactggtagcctggaagaaaagcgcagttgcaattcctatctgtttattataacctttttgaaatctttttgcagACACTTGTGACAGGATTTGCTAGAATTTTCGGACAGCCTGTTGGAATTATTGGAAACAATGGGATTTTATTCAATGAATCTGCACTGAAAGGGGCCCATT

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|29674091|gb|CB670366.1|CB670366
EST:     GCATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACA                         ACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATT
genomic: GCATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACAgtaagtattt ... atttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATT
EST: gi|29640037|gb|CB645046.1|CB645046
EST:     CATAGTTGATGGAAGGGAATTTGATGAATTCAAAAAATTGTATGGAACA                         ACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATG
genomic: CATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACAgtaagtattt ... atttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATT
EST: gi|29640074|gb|CB645083.1|CB645083
EST:     GCATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACA                         ACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATT
genomic: GCATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACAgtaagtattt ... atttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgtatcttgtgcatcgtgtaagtcgttttctttaactttacatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT
                                 ctttaac  putative branch site (score: 3)
                             ttttctttaactttac  TA-rich tract