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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 22
--------gtacttttgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT
          | ||||     |||| ||||   | |    |||| || |||     |||  ||| |  |  | |      | ||||||  |  ||  |   | ||| ||| | || ||||| ||||| ||||| |||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||
atggaaggaaattttttcataagcttacttccctcagtcttatagatgaaac----tatcattactttttgcct------tgttgacactttgtatttccgtcttctcagGCAACATCTCGCGAGGTGAAGCGTCTGGATTCCATTACCAGGTCTCCTGTGTATGCTCAGTTTTCAGAGGCTTTGAATGGTCTGTCCACAATCCGTGCCT

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 24
gtacttttgtgacagctgacttttttaaaaaatat-atattaaagattgtattgt-tagtcctaacttcttgaatcttgacatctcatacctgtcttttccc----agACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT
      || ||  |    ||      |||   ||| || || ||| | | | | | | ||| |   ||   ||||  |||  | |  |||     | || ||    |||  ||  |||| |||||||||||| |||||||||||||||| |||||||| ||||| || |||   ||  || |||| ||| |||| |  || ||||| |
------ttctggaaagaaacaccagaaaagtttattatttttaagttggcactatgttgtcatggtttgaggaat--tgatcttttctactaacatcttgccttgcagAGCACAGCTCGAGAGGTAAAGCGCATGGATTCCATTACAAGATCTCCTGTTTATGCACATTTTGGTGAATCACTGAACGGTTTGTCAAGCATTCGTGCAT

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 23
--------------------------------gtacttttgtgacagctgacttt--tttaaaaaatatatattaaagattgtattgttagtccta-acttcttgaatcttgacatctcatacctgtcttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT
                                 ||| ||  ||||  | ||        |  ||||   | |  |||      | || | ||   | |  | |||  || | ||  || ||   |  ||| |   |||  || ||||| ||  | || ||  ||||||||| |||||| || || || ||||||||||||   |||||||||||||| || ||||  |||||||| |
gtaacctacatactttttaaacgcaatgctatctacattcatgactacagatcgagacatggaaaactgagaccaaaaggaacactgattgtgtcatatctgttgtgtcataac--ctgat-ttttccttattgtagAACACATCTCGGGAAATTAAACGTATGGATTCCACTACAAGATCGCCAGTTTATGCTCAATTTGGTGAGGCATTGAATGGACTATCTAGTATCCGTGCTT

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|66912933|gb|CX099781.1|CX099781
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58692501|gb|CK081188.1|CK081188
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58688905|gb|CK077592.1|CK077592
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58693623|gb|CK082310.1|CK082310
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58613211|gb|CK040923.1|CK040923
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|29621686|gb|CB626697.1|CB626697
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58612973|gb|CK040685.1|CK040685
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAANGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT
                                      tacctgtcttttccc  CT-rich tract