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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT

Basic information

species Oryza sativa
transcript LOC_Os03g11440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 1
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtg--ccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                              | | | ||  ||    ||  |||  | |||  | | | |||  |   |   ||  | |||||     || | ||    || | ||    ||   |   ||  |    ||||||   | ||||  || | |||  ||| |    | | | | | || | || ||||| ||||||||| ||||||||||| ||||||||| |||| || |||||||||||||||||||||||  |||||||||||||||| |||                  
-----------------------------gtaagtgttgtctt--tctaaaaatattgtgatcttcaattatcacaatt--ctaatcgtagc-----atttctctatcaa-gtctgcc-atagtagattataaaccttctgatctgtattta--atatatttgtattgt----gatgcac-attgcatttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCTTGATCGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGTAGT------------------

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 1
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgc-taatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
               | |    | | || || |  || |  | | | |   || |||   |  |  | ||| | |   | |||||     |  |  | |||| |  |     | |  || | |  ||   |   |  |   | ||       |   ||| |||||    |||| | ||  | || |||| ||||| ||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||  |||||||||||||||||||||||||||| |||||||| 
--------------gtaagtgttgtcttattaaaaataatgtaaccttc--aatttatcacaattctaactgttggtggttgttt--catctgcagtctttctgt-agcatttctctatcatagtctgtca---aagtagattat-------aaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACA

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G073498_T03 (Zea mays), 3'ss of exon 2
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgc-taatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
               | |    | | || || |  || |  | | | |   || |||   |  |  | ||| | |   | |||||     |  |  | |||| |  |     | |  || | |  ||   |   |  |   | ||       |   ||| |||||    |||| | ||  | || |||| ||||| ||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||  ||||||||||||||||||||                  
--------------gtaagtgttgtcttattaaaaataatgtaaccttc--aatttatcacaattctaactgttggtggttgttt--catctgcagtctttctgt-agcatttctctatcatagtctgtca---aagtagattat-------aaaccttctgatttgtattgtgatgcacattgcacttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGT------------------

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 2
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtg--ccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                              | | | ||  ||    ||  |||  | |||  | | | |||  |   |   ||  | |||||     || | ||    || | ||    ||   |   ||  |    ||||||   | ||||  || | |||  ||| |    | | | | | || | || ||||| ||||||||| ||||||||||| ||||||||| |||| || |||||||||||||||||||||||  |||||||||||||||| ||||||||||| |||||||| 
-----------------------------gtaagtgttgtctt--tctaaaaatattgtgatcttcaattatcacaatt--ctaatcgtagc-----atttctctatcaa-gtctgcc-atagtagattataaaccttctgatctgtattta--atatatttgtattgt----gatgcac-attgcatttctttactcagGAATGGTGCACAAAAGTTGCTTGGTATCTTGATCGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGTAGTGTAAGCCAACTTGGAACA

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G17950.1 (Glycine max), 3'ss of exon 2
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                                                                                               || | ||| ||  || | |||     || |    |  |   || | |||| | | |    | ||   |||    |||  ||   | |  |  |  |   |||| ||||| ||||| ||| ||||||| ||| |||| ||  |||| ||||| || ||||||||| | |||||||||||||| |||||  | || ||||||   
--------------------------------------------------------------------------------------------gttatgtctca-cggttgtcaattttcctaaggaggttttg---ctcagtcatatatgcttccttttcctattggcattg--acataatttcatctcctctaccagAAATGGTGCACAGAAGCTACTTGGCATCTTGATAGCTGTTGGTGAAGCAGTTGCATATGTTCTTTCTGGAATGTATGGTAGTGTTGGTCAACTTGGAGTG

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s2574g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggcta---ttgatta-aatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                                                                                                     ||| ||||  ||    | ||||  |||  |  | |   ||| |||    | |   |  | || |   |||||     |  || || | || |    | ||||||||| ||||||||| |||| || |||||||| ||  |||| |||||||| ||||||||| | || ||||||||||||||||| ||||| ||||||  |
-----------------------------------------------------------------------------------------------------cag-gaataactgaagtagatttcaatttttttgctagtctaatttccttatgtaacctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggcta---ttgatta-aatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                                                                                                     ||| ||||  ||    | ||||  |||  |  | | | ||| |||    | |      | || |   |||||     |  || || | || |    | ||||||||| ||||||||| |||| || |||||||| ||  |||| |||||||| ||||||||| | || ||||||||||||||||| ||||| ||||||  |
-----------------------------------------------------------------------------------------------------cag-gaataactgaagtagatttcaatttttttgcttgtctaatttccttatgtagcctgttctatatatatacaacaatctgattttctctgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggcta---ttgatta-aatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                                                                                                     ||| ||||  |||   | ||||  |||  |  || |  |   |||    | |      | || |   |||||    |   || || | || ||   | ||||||||| ||||||||  |||| || |||||||| ||  |||| |||||||| ||||||||| | || |||||||||||||| || ||||| ||||||  |
-----------------------------------------------------------------------------------------------------cag-gaataactaaagtagatttcaatttttttaggagttcaatttccttatgtagcctgttctatatatatacaatgatctgattttctcttcctctcagGAATGGTGCACAAAAACTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGCGTTAGCCAACTTGGAGTT

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|33666142|gb|CF297109.1|CF297109
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAAGCTG
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAA-GCTG
EST: gi|58608073|gb|CK036106.1|CK036106
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGT
EST: gi|58670294|gb|CK058980.1|CK058980
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58673187|gb|CK061873.1|CK061873
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|33795495|gb|CF323617.1|CF323617
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58662553|gb|CK051239.1|CK051239
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTG
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTG
EST: gi|29665156|gb|CB661431.1|CB661431
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|29616182|gb|CB621194.1|CB621194
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58672408|gb|CK061094.1|CK061094
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|33795682|gb|CF323711.1|CF323711
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58599868|gb|CK010396.1|CK010396
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58691016|gb|CK079703.1|CK079703
EST:     GTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: GTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58688963|gb|CK077650.1|CK077650
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58689769|gb|CK078456.1|CK078456
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
EST: gi|58693311|gb|CK081998.1|CK081998
EST:     TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCT                         GAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT
genomic: TCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGT

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: 75 (upstream exon), 71 (downstream exon)
Score: 91

GTATCACTCCAATTGTGACATCTGGCATGGTAATGCAACTTCTAGTGGGATCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtatta ... ttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccagGAATGGCGCACAAAAGTTACTTGGTATCCTGATTGCAATTGGGGAAGCTGTGGCATATGTTTTGTCTGGAATGTATGGCAGTGTAAGCCAGCTTGGAACT
                                cgctaat  putative branch site (score: 91)
                                          cttttttaccc  putative PPT
              ttttgattatatttgt  TA-rich tract