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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgattgtttccacccccaatccccaatccatcgattcgattctagggttctcctctctcacctatgcaatctcactctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTCGATTCCATCGGCGGCCTCGACCACGTCAAGCAGGCGCTCTACGAGCTCG

Basic information

species Oryza sativa
transcript LOC_Os06g50050.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G075584_T02 (Zea mays), 3'ss of exon 1
gttcgattgtttccacccccaatc---cccaatccatcgattcgattctagggttctcctctctc--accta---------tgcaatctcactctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTCGATTCCATCGGCGGCCTCGACCACGTCAAGCAGGCGCTCTACGAGCTCG
|| ||  |   |||||||  |  |    ||    |  | || |   |||||||||| | || |||  ||  |         ||   |||| |||  |   |||| |||||||| ||||| |||||||||||||||  |||||||||||| |||||||||||||||||||||||| | |||||||| ||||||||||||||||
gtccg--tccctccacccgtatccgtatccgcctccccaatccccatctagggttcacttcactccgactcaatcctccgctggcgtctcgctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G158136_T01 (Zea mays), 3'ss of exon 1
gttcgattgtttccacccccaatccccaatccatcgattcgattctagggttctcctctctcacctat-gcaatctcactctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTCGATTCCATCGGCGGCCTCGACCACGTCAAGCAGGCGCTCTACGAGCTCG
|| || | |  ||| | | |   |||| ||| |  | |||   ||    |  |||  | |||  |  | |   |||| |||  |   |||| |||||||| ||||| |||||||||||||||  |||||||||||| ||||| |||||||||||||| |||||  ||||||||||||||||||||||||
gtccgttcgcctccccactc--ccccctatcgag-ggttcacctcacttggcctcaaccctcctccgttggcgtctccctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGACTCCATCGGCGGCCTGGACCAGATCAAGCAGGCGCTCTACGAGCTCG
















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|88730849|gb|CI754462.1|CI754462
EST:     AGATCGCCAAGCGCCTCGGCCGCCCCCTCGTCTCCACCACCCCCTACGAG                         GATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTC
genomic: AGATCGCCAAGCGCCTCGGCCGCCCCCTCGTCTCCACCACCCCCTACGAGgttcgattgt ... tctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTC
EST: gi|29622367|gb|CB627378.1|CB627378
EST:     AGATCGCCAAGCGCCTCGGCCGCCCCCTCGTCTCCACCACCCCCTACGAG                         GATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTC
genomic: AGATCGCCAAGCGCCTCGGCCGCCCCCTCGTCTCCACCACCCCCTACGAGgttcgattgt ... tctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgattcgattctagggttctcctctctcacctatgcaatctcactctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTCGATTCCATCGGCGGCCTCGACCACGTCAAGCAGGCGCTCTACGAGCTCG
                                      atctcac  putative branch site (score: 3)
                                       tctcactctaccct  CT-rich tract