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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataagggtttgctcactatgtcaatttaagttgctcttcgcacgtttagaaaagagaacttttagttgatagtaatgcattgttgtgctccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTCAGGGTTAAGAATTCGTACAACCCTAAAGCTCCAGGCACCCTGATCACTA

Basic information

species Oryza sativa
transcript LOC_Os01g70300.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G300862_T05 (Zea mays), 3'ss of exon 7
--tgataagggtttgctcactatgtcaatttaagttgctcttcgcacgtttagaaaagagaacttttagttgatagtaatgcattgttgtgctccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTCAGGGTTAAGAATTCGTACAACCCTAAAGCTCCAGGCACCCTGATCACTA
  | |  |   |    | |  || | |  | | | ||    || |  |   ||||  ||||| |||  | |  |  |  || | ||||   |||||    |||| || ||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| || || |
actaaccatcatgaattgaacatat-agctcatgatgtcagtctcctgaacagaagcgagaaatttaggatcgttattgtggactgtt-cactccaatgcagGTTTTGCATCCACAATCGATGAGACCTGCTAGAGAAGGTGATATTCCAGTTAGGGTTAAGAATTCATACAACCCTAAAGCTCCAGGCACCCTTATTACCA

upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G166366_T01 (Zea mays), 3'ss of exon 2
---tgataagggttt-gctcactatgtcaatttaagttgctcttcgcacgtttagaaaagagaacttttagttgatagtaatgcattgttgtgctccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTCAGGGTTAAGAATTCGTACAACCCTAAAGCTCCAGGCACCCTGATCACTA
    | | |   | | |||||  |||||| | | |||  ||||||    |   ||||| ||||| |||  ||| ||  |  || ||||| |  |||||    |||| || ||||||||||  |||| |||||||||||||||||||||  |||| |||||| ||||||||||||||  ||| |||| ||||||||| || || |
tgaagttgaacatatagctcatgatgtcagtcttagtcactcttc---tgaacagaaacgagaagtttaggttcattattgtggattgt-gcactccaatgcagGTTTTGCATCCACAATTGATGATACCTGCTAGAGAAGGTGATATTACAGTTAGGGTTGAGAATTCGTACAACTGTAAGGCTCTAGGCACCCTTATTACCA

upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G700866_T02 (Zea mays), 3'ss of exon 8
tgataagggtttgctcactat--gtcaatttaagttgctcttcgcacgtttagaaaagagaacttttagttgatagtaatgcattgttgtgctccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTCAGGGTTAAGAATTCGTACAACCCTAAAGCTCCAGGCACCCTGATCACTA
 ||   |   ||| | || ||  |  |  | | | || |  ||    |  |||||  ||||| |||  | |  |  |  |  | ||||   |||||    |||| || ||||||||||| |||||||||||||||||||||||||| ||||| | |||||||||||| |||||| ||||||||||||| ||| | || || |
-gacctgttattgttaacaattgggaagctcatgatgttagtcttctgaatagaagcgagaaatttaggatcgttattgtagactgtt-cactccaatgcagGTTTTGCATCCACAATCGATGAGACCTGCTAGAGAAGGTGATATTCCAGTTATGGTTAAGAATTCATACAACGCTAAAGCTCCAGGAACCATTATTACAA

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|58669471|gb|CK058157.1|CK058157
EST:     CATACTTAACATTTGAAGAGGCAGCAGAACTTGCTTATTTTGGTGCCCAG                         GTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTC
genomic: CATACTTAACATTTGAAGAGGCAGCAGAACTTGCTTATTTTGGTGCCCAGgtatgtattc ... tccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTC
EST: gi|29669913|gb|CB666188.1|CB666188
EST:     CATACTTAACATTTGAAGAGGCAGCAGAACTTGCTTATTTTGGTGCCCAG                         GTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTC
genomic: CATACTTAACATTTGAAGAGGCAGCAGAACTTGCTTATTTTGGTGCCCAGgtatgtattc ... tccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagaaaagagaacttttagttgatagtaatgcattgttgtgctccatgatagGTATTACATCCACAATCTATGAGACCTGCTAGAGAAGGTGATATACCAGTCAGGGTTAAGAATTCGTACAACCCTAAAGCTCCAGGCACCCTGATCACTA
                    agttgat  putative branch site (score: 5)
             aactttta  TA-rich tract