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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG

Basic information

species Oryza sativa
transcript LOC_Os12g06660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                                  | |  |||    ||  | ||   ||  ||| |  | ||| || |   || ||  |     |   | || ||   ||   ||    ||  |   |  ||                 ||||| || |||||  | ||||| || || ||||| || ||||| ||||||||||| || ||  ||||||| || ||||||||||| ||||| ||||| ||||
---------------------------------gcatagcactgtgcattataaaggcatgaaatcccagcttttgat--ggcatttta-----ttgttgaataattccaggcgccggaattgaatttcaattgccg------------cagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S381_21V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttct--tgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgat--aataataatccaa--aattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                                                         |  ||  |      || |  | |  | | || |   | | |        |   |  |||      |  |  ||||||  || |||  | ||   ||| |||||||| |||||||| ||||| || || || || ||||| || |||||||| || || ||  ||||||| || ||||||||||| ||||| ||||||||||
---------------------------------------------------------ctgcattcttagatttgtagtttgctaccttaatgcagtccttcgcgtta-ggcgtcagttgttgtggaagattgatccaaaaatggtgcatgtaatgcagGCCGGTTTCGCGGGAGACGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgata-aaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                                                    |||   |||   |  |||| |   || ||    |||    ||             ||| |       | |  |  | | || |            || ||||| || ||||| || || ||||| || || || ||||| |||||||||||||| || ||  ||||||| || |||||||| || ||||| ||||||||||
----------------------------------------------------aaccttaacttgc-gtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
--------------------gtcat-catcatcatcaactcaatccaattaaccacctctca-caaatcacaa--caacaaca----acaaaccataccttat-gttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacga---taaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                     | || |||    ||   | | ||   || ||    ||  ||  |||   ||   | | | ||    |    |||  |    | ||| | |  |||   | ||   |  | |      | | |||   |   ||||   ||| || |           || ||||| || ||||| || || ||||| || || || ||||| |||||||||||||| || ||  ||||||| || |||||||| || ||||| ||||||||||
gtatgatattaactgttttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaaca--acagcaacgataaaccattg-ataata---ataatccaaaatt-------------------cagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
||   |||  | | |   |  || | | |      ||| ||   |   | |  |    |||||  |   ||||   ||         | |   |    | ||  | |  |  | |   |       ||  || |||||    | ||||  |||||                   ||||| || ||||| || ||||| || || ||||| || ||||| ||||||||||| || ||  ||||||| || ||||||||||| ||||| ||||| ||||
gtatgcatgcttaccgcat--atacgactgtaattctcccatgcaaatcgagcatgctaacaa-tcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                                             |||      | |        | |        |  |  | |      |  || || | |  || ||| | |     ||||   ||| || |           || ||||| || ||||| || || ||||| || || || ||||| |||||||||||||| || ||  ||||||| || |||||||| || ||||| ||||||||||
--------------------------------------------gtcatgg--gccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggca-caaaacc-----taaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S381_18V6.2 (Physcomitrella patens), 3'ss of exon 2
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaa--aattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                                                    |  | |||    ||| | |   | |||| | ||  |    ||   |  | |       |   |||  |  |   |    ||||| |  | ||   ||| |||||||| |||||||| || || || || || || ||||| || |||||||| || || ||  ||||||| || ||||||||||| ||||| ||||||||||
--------------------------------------------------gtagtatcaaatctccacaacc-gtcttct-gtgtctaggtcatgttg-gacctgtgtttaggccaatcaacatgtaggagtaata-tggtgcatgtaatgcagGCCGGTTTCGCGGGAGATGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

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|117251245|gb|CT844082.1|CT844082
EST:     GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAG                         GCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAGgtcatcatca ... caaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
EST: gi|88345352|gb|CI656010.1|CI656010
EST:     GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAG                         GCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAGgtcatcatca ... caaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
EST: gi|86890963|gb|CI305847.1|CI305847
EST:     GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAG                         GCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAGgtcatcatca ... caaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
EST: gi|88576622|gb|CI670767.1|CI670767
EST:     GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAG                         GCCGGGTTCGCGGGCGACGACGCGCCGNGGGCGGTGTTCCCGAGCATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAGgtcatcatca ... caaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
EST: gi|88340655|gb|CI647459.1|CI647459
EST:     GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAG                         GCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTCTGCGACAATGGCACCGGCATGGTCAAGgtcatcatca ... caaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
                            cattgat  putative branch site (score: 4)
                             attgataataataatc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG