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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGCGGCCCCCGCTGCCGCGGCCGGCGCCGCGGTGCCCGGCCCCTGCATCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatctcgcgatctgcatgcctcgctctcgcgcgctggggctctcacgatttcgtttctggcacaccgcag

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G085747_T02 (Zea mays), 5'ss of exon 1
GCCGGCGGCCCCCGCTGCCGCGGCCGGCGCCGCGGTGCCCGGCCCCTGCATCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtac-----ccgatct---cgcg-atctgcatgcctcgctctcgcgcgctggg-gctctcacgatttcgtttctggcacaccgcag----------------------
| |||| || ||| | ||    |||||||| || ||||| || ||||||||||| ||||||||||||| ||||||||||||||| || |||| ||||||||||      || | ||   |||| | |  |   || || |||||||   || | |    | ||||   |||||  ||  ||||  |                      
GTCGGCCGCGCCCCCGGCGCACGCCGGCGCTGCCGTGCCTGGGCCCTGCATCGTGCACAAGCGCGGCAACGACATCCTCCACGATCCGTGGTACAACAAGgtaaggtagccaagctacacgcggagcccccgaccccgatctcgcggtttgcgcgtggactcgatgcggtttc-agcttaccggggcttccattccgtttgggcgcag

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA18G46340.1 (Glycine max), 5'ss of exon 1
-GCCGGCGGCCCCCGCTGCCGCGGCCGGCGCCG-CGGTGCCCGGCCCCTGCATCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgt--acccg--atctcgcgatctgcatgcctcgctctcgcgcgctggggctctcacgatttcgtttctggcacaccgcag----------------------
   ||||||||      || ||||    || || || | ||||| || ||||  || |||||||| ||||| || |||||||||||||| ||||||||||||||  || |    |||    |||| ||  | ||||  |||  |  |     | |    ||||  ||||    || |                           
TCGCGGCGGCCAG-ATCGCGGCGGTTCTCGACGGCGATTCCCGGTCCATGCAAGGTTCACAAGCGTGGCACTGATATCCTCCACGACCCTTGGTTCAACAAggttcactcactgtcttttcatcttca-acttcgccttcgatc--tacacttttttttatttgatttcgctaactctatttatttagttgtttttttatgttg

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA03G01680.1 (Glycine max), 5'ss of exon 1
GCCGGCGGCCCCCGCT-GCCGCGGC-CGGCGCCGCGGTGCCCGGCCCCTGCATCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatctcgcgatctgcatgcctcgctctcgcgcgctggggctctcacgatttcgtttctggcacaccgcag
  |  |  | |||| | || ||||  |  ||||||| | ||||| || ||||| || |||||||||||  ||||||| |||||||| || ||||||||||||||   |  ||||||       |  | |         ||  |     | | || |                      
--CAACCTCGCCCGATCGCGGCGGTTCTCCGCCGCGATTCCCGGTCCGTGCATTGTTCACAAGCGCGGTGCCGACATACTCCACGATCCCTGGTTCAACAAGgt-ttctttctcgcatcacaaaaactttttaacttggctttcctttttttaccag---------------------

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G08110.1 (Glycine max), 5'ss of exon 1
GCCGGCGGCCCCCGCT-GCCGCGGC-CGGCGCCGCGGTGCCCGGCCCCTGCATCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccg--atctcgcgatctgcatgcctcgctctc-gcgcgctg--gggctctcacgatttcgtttctggcacaccgcag-------------------
  |  |  | |||| | || ||||  |  ||||||| | || || || ||||| || |||||||||||  ||||||| ||||| ||||| ||||||||||||||  |    ||| |   |  |     | ||||| || |    |||   |  | | |   | || |  | |  ||  | |||                   
--CAACCTCGCCCGATCGCGGCGGTTCTCCGCCGCGATTCCTGGTCCGTGCATTGTTCACAAGCGCGGTGCCGACATACTCCATGACCCCTGGTTCAACAAGgtttctctcatcacaaaactttttaacttcgctttctgttttctgttagtgttttatcttatcttggcagaaactacacagcttctaacactttatttac

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|29664101|gb|CB660376.1|CB660376
EST:     GCACCGACATCCTCCACGACCCATGGTTCAACAAG                         GACACGGCGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCTC
genomic: GCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatc ... cacaccgcagGACACGGCGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCTC
EST: gi|29671880|gb|CB668155.1|CB668155
EST:     TCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAG                         GACACGGCGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCTC
genomic: TCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatc ... cacaccgcagGACACGGCGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCTC
EST: gi|58671475|gb|CK060161.1|CK060161
EST:     CCGACATCCTCCACGACCCATGGTTCAACAAG                         GACACGGCGTTCCCCATGACGGAGCTGGGATCGCCTTGTGCCTCCGCGGCC
genomic: CCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatc ... cacaccgcagGACACGGCGTTCCCCATGACGGAGC-GGGATCGCCTTG-GCCTCCGCGGCC
EST: gi|58610445|gb|CK038157.1|CK038157
EST:     TCGTCCACAAGCGCGGCACCGACAT-CTCCAGGACCCATGGTTCAACAAG                         GACACGGCCGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCT
genomic: TCGTCCACAAGCGCGGCACCGACATCCTCCACGACCCATGGTTCAACAAGgtacccgatc ... cacaccgcagGACACGG-CGTTCCCCATGACGGAGCGGGATCGCCTTGGCCTCCGCGGCCT