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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG

Basic information

species Oryza sativa
transcript LOC_Os10g40555.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
--gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCT---GATTCGAGTGGTCAGCATG
   ||  |  ||  ||||||  || | || |   | |||   | | ||||||||||||  ||| |||||                       |  |||||||||||||||||||||| |||| |||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||| ||   || || | |||   |    
gtatacagtgttattgttcat-tgcacaa-ataactcctatcagcattttgcattttt--ctcattgtt-----------------------tcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG---

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                       | |   || |  |  | ||  | | | |||||  ||   ||     | | || |    |  | |||    || ||  || |     |  |   | |||| | | | |||||   |||||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||  | ||||  ||   |  ||| |   
gtagttgaacaatttttataaaaaacagacaattttctatctctttttaattcccttatctatctgagcac-cacttcatacactcctgctttcaagaagcttccttgtcggttgctcgttctaactttcgaat-tacccctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTCTATTATGCTGGTAGTCATGGAATGGACATCATTGGGCCTGTTAGACAATCTGTATCTGATAATCACCCAA

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
-------------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                        | |   || |  |  |   || | |  |||||  || | ||     | | || |    |  | |||    || || |||    | | | |   | |||| | | | |||||   |||||| ||||| ||||||||||| |||||||||||||| ||||| || ||||||||  | ||||  ||   |  ||| |   
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcata-cactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgt-tggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S46_31V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcact-ctttgttgactctctcttatgtgtgttttgttctt----tagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
    |||  ||  |      |||   |   |      | |        | | ||    || |  |   ||     |||| ||  || || | | ||     |||| ||||| |||||| || | || ||||| |||||||||||||||||||| |||||||||||||| ||||  | ||  || |||  |  | |   | | |
---tggatcttcagaaattttgtgcgaagttgatttaggtttgtgaagggagttgaagctacaattaagaggtcttcttgtggttgcttcgattttggagcagGTGTTTGAGTTTGTGCAATTGACAGAACTATATTACGCTGGAAGTCATGGCATGGATATCATGGGACCTGCAAAGAGTTCAGATGGGTATCGAGTGAAGG

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S333_42V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------gtaaggaatttatgttcacatgta-----aaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                                                                     |  |  | |||    |   |||||     ||||       | |  |    | ||| | ||    ||  ||| | ||     |  | ||| ||| |  |   |||| |  || || ||| || || | ||| | ||||||||||| |||||||| ||||| |||||||||||||  |     || |||     | ||  | | |
gtactgacaggattcctggtattctgattctgtatcacactctgtccttgagcattggcttgtttctgttaaatccatacattgattcacatgaccttgatgcgaatattttgcagttggatgtagtgtcaaatcaaaattccgagagggatatgc-tgttgggatcgctgt-gcctacagttggtatgtttttggagc---agGTGTACGATTTCGTGCAATTATCAGAATTATATTACGCTGGGAGTCATGGTATGGACATCATGGGGCCTGCGAATGGCTCCGATGGTTTTCGTGTGAAAG

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S141_116V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccc----tgctaaccttttgcatttttcactctt-tgttgactctctct-------tatgtgtgttttgttcttt--------agGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
                                                    | ||    |     ||  |  | || |  |||  |    || ||   ||||   |||||   | |  |  ||| ||   |        | || | || ||  ||| |        |||| |  || |||||| ||||  | ||| |||| ||||| |||||||||||||||||||| ||||| ||||  |  |  ||   || ||  |   |||| |   
gtgaggcttcggtcgttcttttcatagcagtttcctcggtcatggaaaatatttagtgggtggccatcgtacttcaattcttccttcgcattggtacatttttaattttttttttatcatagtgattcatgccaactgaatgtgggcgtattactctatttttgaacagGTATACGATTTTGTGCAACTGTCGGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAA-AGTCAACG--

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgtt--gactctctcttatgtgtgttttgttctt----tagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
     | || ||| || | || | ||  |       |  |       |||||     |   |   ||  ||  |   || |    | || || | ||     |||| ||||| |||||| || | || ||||||||||||||||| |||||||| |||||||||||||| |||| ||  |  ||   || ||   | | | ||    
----tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG---

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtaaggaattta--tgttcacatgtaaaatactccccctgctaacctt-ttgcatttttcactctttgttgactctctct---tatgtgtgttttgttcttt--------agGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
                                                               ||||   || |  | ||| |  | |   | || |   |  |    || ||   |||||   | |||| |||   |  |    |||  |||  ||||||  |        ||||||  || |||||| || |  | ||  |||| || ||||||||||||||||||||||| ||||| ||||  |  |  ||   || ||  |   |||| |   
gtgagtctttggtccgtcgtttctctatgtagtcgaaaacgttgtgtggatgaccattgtacttaagtctttcaattattctcg-gcattttgcttcgttttttttttttcttttttttttttttttttgctgaacataacccaatatcggtgaattgttcgattctgaaacagGTTTACGATTTTGTGCAATTGTCGGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGCAAAAAGTTCAAGTGGTTTTAA-AGTCAACG--

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|58607388|gb|CK035421.1|CK035421
EST:     TGGCGGGACTTTTTCCCACTGCGATCATTAGTGGAAGATCTCGTGATAAG                         GTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGA
genomic: TGGCATCACTTTTTCCCACTGCGATCATTAGTGGAAGATCTCGTGATAAGgtaaggaatt ... tgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                    tgttgac  putative branch site (score: 3)
                                          ttttgttcttt  putative PPT
       atttttca  TA-rich tract