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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g02530.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
---cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
    |  | | |||  ||     | ||| | |   |  |  | |   |   |||   | | | | |     ||   | |      || || | |||  | |||||||| |||||| | ||||| ||||||||||||||||||||||| || |||||||| |||||||||||||||||||| || ||||||
gctacaataagattcatatttgtt-ttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttt--tgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
cctgttatatttgtagaaactattgcac-tgcttgctgtactttgtaaatcactattaagtt--gtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
  |  |   ||  || ||  |   |||  |||||  |  | | | ||| ||  | ||   ||   ||     | ||  || |     ||| | | |  | |||||||| || ||| | ||||| |||||||||||||||||||| || || |||||||| |||||||||||||||||||| || ||||||
-ttagtcagttattaaaagattaagcatatgctt--ttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagtt--gtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
   || |  | |  | | |  |      |||||    |  | |     || || ||   ||   ||  |  | ||  || |     ||| | | |  | |||||||| || ||| | ||||| ||||||||||||||||||||||| || ||||| || |||||||||||||||||||| || ||||||
--agtcagttattaaaagatcaaacatatgcttttcattgtataattctctctttttgtttcaatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
---cctgttatatttgtagaa-actattgc--actgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatca------cgggatttccttt--ttgatt--cagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
        |  || | | |||  |||||    |   |||| |     || || || |  |  || ||     |   |||  |||      |||  |||  | |  |||| |  ||||| || || |||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||||| || ||||| || || |||
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
--cctgtta-tatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgatt-cagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
    ||  | ||||| |       ||  |  ||| || |      |  |  |   |  ||  |   |  | || | |  || |||   | |||    ||| ||||| || || ||| | ||||||||||||||||| ||||||||||| || ||||||||||||||||| || || ||||| || || |||
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttt-tgacatggg---tacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ18240 (Selaginella moellendorffii), 3'ss of exon 6
cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
                                    ||||  |||   |||||   ||      ||  | |||  |       | ||  | |     ||||| || || ||  | ||||| || |||||||| |||||||||||||| |||||||  ||||| || || |||||||| || || |||
------------------------------------gtaccgtgt---tcacttacaaaacaacactttgatgatttgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
                                    ||||  |||   |||||   ||      ||  | ||   ||      | ||  | |     ||||| || || ||  | ||||| || |||||||| |||||||||||||| |||||||  ||||| || || |||||||| || || |||
------------------------------------gtaccgtgt---tcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

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|58684751|gb|CK073438.1|CK073438
EST:     GAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG                         GCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATG
genomic: GAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctg ... tttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
                                      tttcctttttgattc  CT-rich tract
       tattaagtt  TA-rich tract