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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctaaccccatcctttttccttttcttttaaaaagtttctgctataatatcacatggtggtgataatagatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 3
gtctaaccccatcctttttccttttcttttaaaaagtttctgctataatatcacatggtggtgataatagatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
           |   | |    ||   | |  ||  |   |   |  ||| |   |  |   ||   || |   || |    |   ||||| ||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||||||
----------gtttatatatagttcactctggaagttacttaaaaagataccctcttctatggaagttacactaatacatg-accacagGTTGCTTTGAAATTTGAGCACCGAAACAGCAAGGGCTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
-----gtctaaccccatcctttttccttttcttttaaaaagtttctg------ctata--atatcacatggtggtgataatagatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
      |  |         ||| || ||    || ||  |  |  |       |||||   ||| | |   || |  |  |   |  |   |  | || ||||| ||  | || || |||||| | ||||| || |||||||| ||||| ||||| |||||||||||||| || ||
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgt-ttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
gtctaaccccatcctttttccttttcttttaaaaagtttctgctataat--atcacat-ggtggtgataat-agatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
        | || |   ||  |||     ||  ||  || | | || ||   |||| |  |   || || | | | |||||| ||||   |||||||| ||||| || |||||||| || || || || ||||||||||||||||| |||||||||||||| || | 
-----gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcata--acagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtctaaccccatcctttttccttttcttttaaaaagt-------ttctgcta-taatatcacatggtg---gtgataatagatggattctcatatt-------gcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
                         |||    |   || | || | | |  |    |    |       ||  || | ||   |  | | |||   |  |  | | |  || |||  | ||       |||||||||||| || || || || || | ||| ||||||||||||||||| ||||| || |||||||||||||| | 
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------gtctaaccccatcctttttccttt----tcttttaaaaagtttctgc-tataatatcacatggtggtgataatagatggatt----------ctcatattg------------cagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
                     ||    | | |    |||  |       | |||  || |   ||||| |||   |||      | |||||  |  ||| | |           ||||||||            ||||| || ||||| |||||||| || |  |||||||| ||||||||||| ||||| ||||||||||| ||||| | 
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtctaaccccatcctttttccttttcttttaaaaagtttctgctataatatcacatggtggtgataatagatggattctcatattg-cagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
                     |   || ||  ||  |||   |  |   ||    |  |  |   |   | ||       || ||| ||||| |||||||| || || ||| | | |||||| || ||||| ||||| ||||| ||||||||||||||||| | 
--------------------gtagactgttcgaagatttgctcagttggattggctcttt-tctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtctaaccccatcctttttccttttcttttaaaaagtttctgctataatatcacatggtggtgataatagatggattctcatattg-cagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
                     |   || ||  ||  |||   |  |   ||  |    |  |   |   | ||       || ||| ||||| |||||||| || || ||| | | |||||| || ||||| ||||| ||||| ||||||||||||||||| | 
--------------------gtagactgttcgaagattttctcagttggattgctc--ttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|29629024|gb|CB634035.1|CB634035
EST:     GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAG                         GTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
genomic: GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAGgtctaacccc ... catattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
EST: gi|88720002|gb|CI745301.1|CI745301
EST:     GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAG                         GTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
genomic: GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAGgtctaacccc ... catattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAG                         GTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
genomic: GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAGgtctaacccc ... catattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
EST: gi|58661787|gb|CK050467.1|CK050467
EST:     GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAG                         GTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT
genomic: GCAGAAGGGTTTCTGGTGGAACTGATCGCACTGGAGCTGATGCTATCGAGgtctaacccc ... catattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctgctataatatcacatggtggtgataatagatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
                                         ttctcat  CT-rich tract
         tataatatca  TA-rich tract