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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_Os04g52900.2
intron # 23
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 74 (downstream exon)
Score: 29

GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTGTATGCTCAATTTTCAGAGGCATTGAATGGTCTGTCTACAATCCGTGCCT
                                      tacctgtcttttccc  CT-rich tract