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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctgtaacattcatgtaatatgtaattcgtaaaagtctaatttggaatcatagccttaaacaatctctgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGGACCTGAAAGGGAAAGGGCGATGTAAAGACATAGTGAGTAGGAAGCGGCT

Basic information

species Oryza sativa
transcript LOC_Os07g17400.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G011562_T01 (Zea mays), 3'ss of exon 3
gtaatctgtaacattcatg--taatatgtaattcgtaaa--agtctaatttggaatcatagccttaaacaatctctgcc-ttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGGACCTGAAAGGGAAAGGGCGATGTAAAGACATAGTGAGTAGGAAGCGGCT
||| ||| || | |  |||       |||||  | |  |  | |||  |||||| |   |  || | |     ||  || || |||| || ||||| || || || || ||||||||| |||||||||| ||||||||||| |||||||| || ||||| || || ||||||||||||| | || |
gtagtctctagcctatatgggcgtgttgtaacccatgcatcaatctgctttggactggaattctcataagccttcatccattgcagCAATTATCTATCCGATTCTGCAGCAGCTTGAGAGTAGTTTGATCGAGAGGGACCTAAAAGGGAAGGGCCGATGCAAGGATATAGTGAGTAGGAGGAGGAT

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G439168_T02 (Zea mays), 3'ss of exon 4
gtaatctgtaacattcatg--taatatgtaattcgtaaa--agtctaatttggaatcatagccttaaacaatctctgcc-ttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGGACCTGAAAGGGAAAGGGCGATGTAAAGACATAGTGAGTAGGAAGCGGCT
||| ||| || | |  |||       |||||  | |  |  | |||  |||||| |   |  || | |     ||| || || |||| || ||||| || || || |||||||||||| |||||||||| |||||||||||||||||||| || ||||| || || ||||||||||||| | || |
gtagtctctagcctatatgggcgtcttgtaacccctgcattaatctgctttggactggaattctcataagccttcttccattgcagCAATTATCTATCCGATTCTGCAACAGCTTGAGAGTAGTTTGATCGAGAGGGACCTGAAAGGGAAGGGTCGATGCAAGGATATAGTGAGTAGGAGGAGGAT

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171967_T01 (Zea mays), 3'ss of exon 3
gtaatctgtaacattcatg--taatatgtaattcgtaaa--agtctaatttggaatcatagccttaaacaatctctgcc-ttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGGACCTGAAAGGGAAAGGGCGATGTAAAGACATAGTGAGTAGGAAGCGGCT
||| ||| || | |  |||       |||||  | |  |  | |||  |||||| |   |  || | |     ||| || || |||| || ||||| || || || || ||||||||| |||||||||| |||||||||||||||||||| || ||||| || || ||||||||||||| | || |
gtagtctctagcctatatgagcgtgttgtaacccctgcatcaatctgctttggactggaattctcataagtcttcttccattgcagCAATTATCTATCCGATTCTGCAGCAGCTTGAGAGTAGTTTGATCGAGAGGGACCTGAAAGGGAAGGGCCGATGCAAGGATATAGTGAGTAGGAGGAGGAT

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|33684776|gb|CF313015.1|CF313015
EST:     TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATG                         CGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
genomic: TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATGgtaatctgta ... tgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
EST: gi|33685850|gb|CF314089.1|CF314089
EST:     TAGCTCAGTATCAACGTATGAAAGGCGTGCAGGCCTTAGAGAATTCTATG                         CGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
genomic: TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATGgtaatctgta ... tgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
EST: gi|58692534|gb|CK081221.1|CK081221
EST:     TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATG                         CGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
genomic: TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATGgtaatctgta ... tgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
EST: gi|33684777|gb|CF313016.1|CF313016
EST:     TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATG                         CGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG
genomic: TAGCTCAGTATCAACGTATGAAAGGCGTGCAAGCCTTAGAGAATTCTATGgtaatctgta ... tgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattcgtaaaagtctaatttggaatcatagccttaaacaatctctgccttccagCGATCATCTACCCTATCCTTCAACAGCTTGAGGGTAGTTTGATTGAGAGGGACCTGAAAGGGAAAGGGCGATGTAAAGACATAGTGAGTAGGAAGCGGCT
            gtctaat  putative branch site (score: 3)
                                         tctctgccttcc  putative PPT
       taaaagtctaattt  TA-rich tract