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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA

Basic information

species Oryza sativa
transcript LOC_Os02g19510.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006507_T04 (Zea mays), 3'ss of exon 2
gtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
          ||      ||||     || |  ||   |||| |||   | | ||    |  |   |  ||  |||||     | ||  ||| ||      ||| | |||    |   ||| |   || ||| | |   | |||  |||||| | ||  || |||  ||| || ||||| ||||||||| ||||||||  ||||||||||||| ||||||||| | ||| | ||| |||| ||| |||||||| | |||||||||||||| ||    
---------gtatgttcactaccac--atccacaa--atttcattttaatatataaa--tagtccttgtttagtctgt---atatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcagCAGCATGCCAAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAAC---

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 2
gtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
||| |||   |||  || | ||    | |  | | | |||  | ||| || | |||   | | || || | || ||                  ||       |||       |||| | ||  ||||||         | ||| ||||||| | ||  ||  ||  | || ||||||| ||||||||| |||||||| ||| |||||||||| ||||||||||| ||||| ||| |||| ||| |||||||| | |||||||||||||| || |||
gtatgttcactaccacatccacaaact-tcataagcagttcttgttcagtctgtagatttaactgctagtgtacct------------------aatgttgggcaa-------ttttatgtcctcggtgcc-------actcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 2
gtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
          ||      ||||     || |  ||   |||| |||   | | ||    |  |   |  ||  |||||     | ||  ||| ||      ||| | |||    |   ||| |   || ||| | |   | |||  |||||| | ||  || |||  ||| || ||||| ||||||||| ||||||||  ||||||||||||| ||||||||| | ||| | ||| |||| ||| |||||||| | |||||||||||||| || |||
---------gtatgttcactaccac--atccacaa--atttcattttaatatataaa--tagtccttgtttagtctgt---atatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcagcagCATGCCAAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA

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|29641723|gb|CB646730.1|CB646730
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58687148|gb|CK075835.1|CK075835
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58666569|gb|CK055255.1|CK055255
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88696183|gb|CI739758.1|CI739758
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58601351|gb|CK011879.1|CK011879
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88356602|gb|CI626217.1|CI626217
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88396973|gb|CI578122.1|CI578122
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
                          atttaat  putative branch site (score: 4)
                  acattgtaatttaatt  TA-rich tract