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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG

Basic information

species Oryza sativa
transcript LOC_Os03g50885.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 1
gtaagctgtttggatc-tcagggtggtttccgtttac-cgaaatgct--gcatttcttggtagcaaaac--tgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
||||||     |  |  |||     |||   |   |  | |  | ||  |    |  |||   |  |||    |          | |||||||||||||| || || || || || ||||| |||||||||||||| || || ||||| |||||||| |||||||||||||| ||||| ||||||||||
gtaagccaccggtttggtcacatctgttcttgagaatgcaaggttctcggtggctgctggggccctaacaacaacaccaacctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
|||||||      | | | |  | ||| || |  ||  ||    |    |||    |  |  |||         || || ||||||||||||||||| || || || || ||||| |||||||||||||| || || ||||| |||||||||||||| ||||| || ||||| |||||||| |
gtaagct------accgccgatttgttccc-tgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
-----gtaagctgtttg--gatctcagggtggtttccgtttaccgaaatgctgc--------atttcttggtagcaaa-actgaggtggtttgtgt-cagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
      |||  ||   |  |  |   | ||||   |||     |     | ||         |  |  || | || |   ||| |  |   |||   |||||||| || || || |||||||| ||  | ||||| ||||||  ||| || ||||| || |||||||||||||| |||||||| ||||||||||||    
tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcagcgcgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
----------gtaagctgtttggatctcagggt--ggtttccgtt--taccgaaatgctgcat--ttcttggtagcaaaactgaggtg-gtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
          ||    | |   |   | |       | ||  | |   |    | || || ||  |||  ||   |  || |||  |    |||   |||||||| |||||| |||| ||||| ||| ||||||| ||||||||||| || || || ||  | |||||||| || ||||| || ||||| ||||| ||||
gcatagcactgtgcattataaaggcatgaaatcccagcttttgatggcattttattgttgaataattccaggcgccggaattgaatttcaattgccgcagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
------------gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggta----gcaaaactgaggtggtttgtgt-cagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
             | |  | |   |  |  |   ||| |   |  ||    |          ||| |  |    |   || |  ||||  |||    |||||||| ||||| ||||| ||||| ||| | ||||| |||||||||||||| || |||||  | ||||| || || |||||||| ||||| ||||||||||
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
----gtaagctgtt-tggatctcagggtggtttccgtttaccgaaat--gctgcatttcttggtagcaaa---------actgaggtggtttgtgt-cagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
      | ||| |  |||   ||| | |  |     |  |  ||  |  | ||   |     | |  |||         | || ||||  |||    |||||||| ||||| ||||| ||||| ||| | ||||| |||||||||||||| || |||||  | ||||| || || |||||||| ||||| ||||||||||
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------gtaagctgtttggatc-tcagggtggtttccgtttaccgaaatgctgcat--ttcttggtagcaaaactgaggt--ggtttgtgt----cagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
                                                                                  |||   ||| ||     |||  ||  | |     || ||     ||||||  | |     | |  || | ||||  ||||| | |    |||||||| ||||||||||| ||||| ||| ||||||| ||||||||||| || || || ||  | |||||||| || ||||| || ||||| ||||| ||||
gtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S381_18V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtg-gtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
                  || |   ||   | ||  |||  | |  |      |    |    ||      |||| |  | |  ||||  | |    ||||| || ||||| ||||||||||| ||| | ||||| || |||||||| ||||| || ||  | ||||| ||||| ||||| || ||||| ||||||||||
gtagtatcaaatctccacaaccgtcttctgtgtctaggtcatgttggacctgtgtttaggccaatcaacatgtaggagtaatatggtgcatgtaatgcagGCCGGTTTCGCGGGAGATGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
                     |||   ||| |    ||   |  ||    | ||| |         | ||||  || |  |||||||| || |||||||| ||||| |||||||| || || ||||||||||| ||||| ||    ||||| || |||||||| |||||||| |||||||| |
---------------------gtgcgctcc-tggcgcggtttcttgtggattttgatccgg-----ggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
                     |||   ||| |    |||  |  ||    | ||| |         | ||||  || |  |||||||| || |||||||| ||||| |||||||| || || ||||||||||| ||||| ||    ||||| || |||||||| |||||||| |||||||| |
---------------------gtgcgctcc-tggcgcgatttcttgtggattttgatccgg-----ggggtgtgtttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|58601004|gb|CK011532.1|CK011532
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58671237|gb|CK059923.1|CK059923
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGTGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58599400|gb|CK009928.1|CK009928
EST:     GAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: GAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58677367|gb|CK066054.1|CK066054
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|11610538|gb|AU166214.1|AU166214
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58610538|gb|CK038250.1|CK038250
EST:     CCGAGGATAT-CAGCCCCTCGTCTGCGATAATGGAACTGGTATGGGCGAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGGCTGTCTTCCCCAGCATTGT
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCA-GGGCTGTCTTCCCCAGCATTGT
EST: gi|4968767|gb|AU065671.1|AU065671
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|88719767|gb|CI743277.1|CI743277
EST:     GATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: GATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58589384|gb|CF987692.1|CF987692
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58596324|gb|CK006852.1|CK006852
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58675220|gb|CK063907.1|CK063907
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58653290|gb|CK041970.1|CK041970
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCANGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|396941638|gb|HO188295.1|HO188295
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|66913140|gb|CX099988.1|CX099988
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
EST: gi|58661439|gb|CK050119.1|CK050119
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAG                         GCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTC

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: 63 (upstream exon), 73 (downstream exon)
Score: 99

GCTAGCATAAGATGGCTGACGCCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtt ... tttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG
                   atttctt  TA-rich tract