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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG

Basic information

species Oryza sativa
transcript LOC_Os07g08880.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 2
atgctttgctggcctatgctatctattaaattgatttatgtat-tgcattaatatcatcattttatttgattttctcatccctttactaaca-atatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
||   | |    | | |  ||  | |  |  |  ||  |  || || || |  ||  | | ||  |||  |  ||| ||| |||   ||| | || || |||||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||
atagatgg--aactttttttacttgtatatgtatttcttaaatctgaatcatcatttttacttgttttattcctctaatctcttctgtaaaacatgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattt--tctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
     | |   |     ||| | | ||| | |     |  | | | ||   ||||   ||| |   |  | |  | | |    ||||  |     ||  |||||  || || ||||||||||| ||||| ||||||||||| ||| ||||||||||||  ||| |||| ||
-aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatct-tatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
----atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
    ||  ||   ||   | |  | |  |||   || ||  |  | ||     ||    |     | | |||| |||   ||   |||  |  |  | || |||||||||||||||||||||||| || || || |||||| | ||| | ||||| ||||| || ||||| ||
gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaa-attgatttttt--ctgtttg-cagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
--atgctt-tgctggcctatgc-tatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
  ||   | |       |||   ||| ||| |  ||    | ||| |     |  |     |   ||| |  |  |   ||||   |      |  | || ||| |  |||||||| |||||||| ||||||||||||||| | ||| | ||||||||    |||   || ||
atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactcc---gctgtttg-cagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------atgctttgc-tggcctatgctatctattaaattgatttatgtattgcatta---atatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
                                                                              ||| |  || | |  | | || |    |  | ||| | | |  | |  ||    |  | |  | ||| |    ||   | ||  |||         | |  |||||  ||||||||||||||||||||||| |||||  || | ||| |  ||||  |    |||   || ||
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 3'ss of exon 2
-atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttat-ttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
     || |||      |   ||||     |  |||   |  | |  |  |  ||| |  |    | ||  |  ||    || |  |||     |||| ||| |  ||||||||||| ||||||||||||||||| ||| | ||| | ||||||||    |||   || ||
cgattttggctttgtagttacatcttcctgaaagatgccttaaatagaaaacaatccttgtgccgtattagtaatcgtgaccttcaactggtg-tatg-cagTTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------------atgctttgctggcctatgctatctattaaattgatttatg-tattgcattaatatcatcattttatttgattttctcatccctttactaa---caatatgac----agGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
                                                                       | |||  || |     | | | |  | |    | || |  | ||    |  | |    | ||   ||  || |||  |    |||| ||   |  ||| ||    ||||  |||||||||||||||||||||||||| || ||  | ||| | || || |||   |||   |||||
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgtgttcttatcaagcttctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

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|218504563|gb|FG952376.1|FG952376
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|3462559|gb|AF074797.1|AF074797
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCGGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|58679044|gb|CK067731.1|CK067731
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|86261244|gb|CI014311.1|CI014311
EST:     CCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: CCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|33822155|gb|CF336893.1|CF336893
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATC
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATC
EST: gi|218497932|gb|FG957265.1|FG957265
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|86498011|gb|CI140644.1|CI140644
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|29686487|gb|CB682762.1|CB682762
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|58603106|gb|CK013634.1|CK013634
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|38471848|gb|CF955979.1|CF955979
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
                                      tactaac  putative branch site (score: 0)
     atatcatcattttatt  TA-rich tract