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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 5
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||||||||||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||| |||||||||
gtacagatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 1
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||| ||||||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||||||||||| |
gtacaaatttatgggacagttgtaaagcctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctaaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G175541_T02 (Zea mays), 3'ss of exon 3
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    || | ||||||||   |||| |  | | || ||||||||||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactatgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 5
--------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                 ||||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||||||||||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||| |||||||||
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 3
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    ||  |||||||||   |||| |  | | || ||||||||||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaacggtgcataat---cttgta--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 5
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||||||||||||||||||||  ||||||||||| || ||||  || ||| |                             
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCACATGTGTGGGGACCCAAATTTAGTCCTTAG-----------------------------

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 3
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                || || | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||||||||||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||
gtacaaatttatgggacagttgtaaacccttttatatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 6
gtacatttttctggc-tccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG---------------
||    |||  | |  | |||   ||       | |||    |    ||  || ||  | |||  ||| ||    ||  |||    |  ||| | |||||     ||    | | | |     |  | ||  |  | | ||||    |               
gtttgctttcatagagttcactgatgagggtaat-atatccatatccaaccatgtttcagTTTG-CTTACTCTGTGTAATGGGTC-TACTATTTATGGGGTGAAAAACATCGATGTCC-CAGAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTT

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 4
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                 |||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||| ||||||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||||||||||| |
gtacaaatttatgggacagttgtaaaccctctaacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctaaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 2
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| |||   || ||||| |||||   ||| |  |   || | ||||||||||||||||||| |||||||| || || || || || ||||| || || ||||||||||||||||||||||
gtacgaatctgtgggacaattgtaaatcccattacatatatttagttccccatttg-tttttgttgcaactgtgcgtaata--tttgga--tacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 4
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||    || ||||||||||   |||| |  | | || ||||||||||||||| ||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGAGTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 12
---------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                     |||      ||    ||| || ||| ||| |||   ||  |||  |||||   ||| |  |   || | ||||||||||||||||||  |||||||| || || || || || ||||  ||||| ||||||||||||||||||||||
gtacgaatctgtgggacaattgtaatcccatcacattccccatttg-tttttgttgcaaccgtgtgtaata--tttgga--tacactgtttgaagGTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCAGTTTGCCTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||     | ||||||||||   |||| |  | | || ||||||||||||||||||||| ||| ||||||| || ||||| || ||| | ||||||||| ||||||||||||||||||
gtacaaatttatgggacagttgtaaatcctcttacatgtatttagttccccatttgattt-tgatccgactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 2
---------------------gtacatttttctg-gctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                     ||| ||     |    ||| || ||| ||| |||   ||  |||  |||||   ||| |  |    | | ||||||||||||||||||  |||||||| || || || || || ||||| ||  | ||||||||||||||||||||||
gtacaaatttgtggaacacttgtaaatcccattacattccccatttg-tttttgttgcaaccgtgtgtaata--tttgga--tacgttgtttgaagGTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCACCTTCATAGAGTTCACTGATGAGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
-------gtacatttttctggctc-cacacttgctttctgtgataattgtgcataata-atcttgaaatttttctttctga-agGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
        ||  || ||   |||| ||    ||   ||  | ||  |  |   |  |   ||||    | |||  || | | ||||||| |||||||| || || || || || || || || ||||| ||||| |||||||||||||||||||| |
gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 4
----------gtacatttttctggctccacacttgctt-tctgtgataattgtgcataataatc-ttgaaatttttcttt----------ctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
          ||    | || |   |  |  |  | || | ||    ||| | | ||  |  |  || |   ||| ||||           |||||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||| | || || ||||||||||
gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtttgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG

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|29646833|gb|CB651840.1|CB651840
EST:     GTCACTGAAGAGCAATTGGCAGCACTATTTATCAACTGTGGACAG                         GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCT
genomic: GTCACTGAAGAGCAATTGGCAGCACTATTTATCAACTGTGGACAGgtacattttt ... ctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCT




















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), 51 (downstream exon)
Score: 29

GTCACTGAAGAGCAATTGGCAGCACTATTTATCAACTGTGGACAGgtacattttt ... ctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
                                        tttttctttct  CT-rich tract
                         ataataatcttgaaat  TA-rich tract