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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctcctctgaaccattctctcccaaattccattgttcttcagagtgagataataaatatcttgtcaagtccaaatatgtttagcaagcataagcatttgatgtttaattggactaacaagtattatacttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGG

Basic information

species Oryza sativa
transcript LOC_Os11g01439.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 6
gtaagcatctcctctgaaccattctc----tcccaaattccattgttcttcagagtgagataataaatatcttgtcaagtccaa---atatgtttagcaagcataagcatt-------tgatg-tttaattggactaacaagtatta-tacttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGG
|| ||  |||| ||   | ||| |      | |    |  ||| || ||||||||||| | |  ||   | ||| |  ||  ||   || | | |    | |||||   |        ||||| ||| |||| |||||| ||  | | ||| |||| |||||||||||||||||| ||||| ||||| ||||| ||||||||| || | |||||||||| |||||||||  | ||  | || |||||||| | ||| || 
gttagtgtctcgtcctcatcatacctagtattctctctaacatagtacttcagagtgaaacagcaatatttttgcctggtttaagatatgtatgtgatgaacataattttacccaaagtgatggtttcattgtactaactagcgtcaatacatatgccagAGTGGAGCAGAGTGTCTATGCACTACTCCGTACAAGAGACATGACCGTCTCACGCTACAAGGAGTACGGGATCCCATTTGACTGGCTGTCAGATTCTGGA

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 3
gtaagcatctcctctgaaccattctctcccaaattccattgttcttcagagtgagataataaatatcttgtcaagtccaaatatgtttagcaagcataagcatttgatgtttaattggactaacaagtatta-tacttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGG----
                                    |||| ||     |    ||||| |  ||    ||   |    || | |  | |  |   ||           |||| |||| |||||| || || | |||||||| ||||||||||||| |||| ||||| ||||| ||||| ||||||||| || |  ||||||||| |||||| ||  | || || || ||| |||||| ||||||     
---------------------------------caacatttttgcctggttcaagata-tgtatg---tgatgaacataattttactcaaaagtgatg----------gtttcattgtactaactagcatcaatacttatgccagagTGGAGCAGTGTGTCTATGCACTACTCCGTACAAGAGACATGTCCCT--CACGCTACAAGGAGTATGGGATCCCAGTTGACTGGTTGTCTGATTCCGGAGTAG
















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|29630415|gb|CB635424.1|CB635424
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|58695568|gb|CK084255.1|CK084255
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29646000|gb|CB651007.1|CB651007
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29667941|gb|CB664216.1|CB664216
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29612706|gb|CB617719.1|CB617719
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29612723|gb|CB617736.1|CB617736
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29613986|gb|CB618999.1|CB618999
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|38475765|gb|CF959898.1|CF959898
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGA
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGA
EST: gi|29668095|gb|CB664370.1|CB664370
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|58609462|gb|CK037495.1|CK037495
EST:     AAGCGGGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
EST: gi|29629417|gb|CB634426.1|CB634426
EST:     AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAA                         AGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC
genomic: AAGCTTGCATGTGAAGAAGCTCTCAAGAAGATGTATTCCTTGCTTGAAAAgtaagcatct ... cttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagcataagcatttgatgtttaattggactaacaagtattatacttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGG
                            gactaac  putative branch site (score: 1)
            atttgatgtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctcctctgaaccattctctcccaaattccattgttcttcagagtgagataataaatatcttgtcaagtccaaatatgtttagcaagcataagcatttgatgtttaattggactaacaagtattatacttatgtcagAGTGGAGCAGAGTGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA