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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag

Basic information

species Oryza sativa
transcript LOC_Os08g23810.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G070422_T03 (Zea mays), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag
 ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||| || ||||  |||||| |||  |||  |      ||||      |||  |  |  ||  |    | ||| ||  |||| | |  ||||
ATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTACATGGGTGCCGgtatgttgatcagactcttacagatttctttg-----cattgaacacttt--tgctgatcgattgtcttatgtagtattcttctttgacag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 1
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag
 ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||| ||| || ||||  ||| ||  ||  |||  |      ||||  |   |||  |  |  ||  |    | ||| ||  |||||| |  ||||
ATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCAAAGGCACTTGCTGCGGCTGGTGCTGAAATGCTTGTTGGTACATGGGTGCCGgtatgttgatcagacttttaaagatttctttg-----cattggtcacttt--tgctgatccattgtcttatgtagtattctactttgacag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 2
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaact---cttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgca--cag---------------------------
 ||||||||||| || |||||||||||||| |||||||||||||| |||||  |||| || || || || |||||||||||||| || |||||||| |||||||||  ||   |||     ||  ||  |   |  | |   | |||  |||| | ||       |  | |    | ||  | |||  |    |||                           
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatattactgattctggtgtagtgtgtttgtacattgtttacttttaccctgaaatgatggcatctctgtgaaatatacaagtggtcaggtactaactttgaacattttcatgcag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat----ccaactct--tgcagtgt---tcaatagggatcatttttttt-----------tttcctctttgtcattcacttaatggagagttctacctgcacag------------
 ||||||||||| || |||||||||||||| |||||||||||||| |||||  ||||||| || || || |||||||||||||| || |||||||| |||||||||  ||    |  | |||  || |||||   |  | |  | | | ||||              ||  |||| ||| ||  ||     |    |||||| || |  |             
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatatcactgattctggtgtagtgtgtttgcacattgtttacttttaccctgaaatcatgttatctctgtgtaatatacaagtggtcaggttctaacttcgaacattttcatgcag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcattttttt--ttttcctctttgtcattcacttaatggagagttctacctgcacag--------------------------------------------------------------------------
 || |||||||| ||||||||||||||||| ||||| ||||||||||||||  |||||||||| || || ||||||||||||||||| |||||||| |||||||||   |       ||    |    ||| || | |  |   ||  | | |   ||    |    ||   ||  || || |      |||                                                                           
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 4
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcattttttt--ttttcctctttgtcattcacttaatggagagttctacctgcacag----------------------------------------------------------------------------
 || |||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||| || || ||||| || |||||||| |||||||| |||||||||   |       ||    |    ||| || |||  |   ||  | | |   ||    |    ||   ||  || || |      |||                                                                             
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAAGCTCTTGCTGCAGCAGGAGCTGAGATCCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtatctatcagttgatatacgaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttttccagtccttttgtgctgatacatttactaactgtgaaccatttctatag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag
 |||||||||||  | |||||||| ||||||||||| ||||| || |||||  |||||||||||||||| ||||||||  | ||||| || ||||| |||||||||   |     |   || |  || | |          ||  ||  |    | |   |  |  | ||||||  || ||||  |     
TTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGACTTGGGTTCCTgtaagtcatttttggttcagctgcttttagt------ttccttcattgctaaattatactaacctatgaatggatggt-ctactag-----

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat----ccaactcttgcagtgttc-----aatagg--gatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag---------------------------
 || ||||| || || |||||||| ||||| ||||| |||||||| |||||  | ||||||||||| || |||||||||||| |||| ||||||||||||||| ||  ||    | ||||  |  | |   |      ||||   |||   |   || |  |  |  |||  |   | |  |  |   || ||  |    |                            
ATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCACATGGGTGCCTgtatgtaaattattctaacttctttaattgacttgtggatagactgattcatgagttctggcaacaatgttttgttccttgtaaaatattttattttttaatgataataataattttttattttcatag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 5'ss of exon 3
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatcca-----actcttgcagtgttcaatagggatcatttttttttttcctctttgtcat---------tcacttaatggagagttctacctgcacag
 || |||||||| ||||||||||||||||| ||||| |||||||| || ||  ||||||| ||||| |||||||||||||||||||| |||||||| |||||||||  ||  |     ||   |    |  ||       ||||     |  | |   |  |||||          | ||| | |||  || ||  | ||   ||
CTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCACATGGGTTCCTgtaagtaaattaatgatcacatatatcattctctgctttaatcacagagtaatctgagccatgtcaaaccattggattactaactgggaagctc--cttgtgtag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag---------------------
||| ||||| || || || |||||| | || | ||||||||| ||||| || ||||| || || ||||| |||||||||||||| || || |||||||| |||||    |  |||  |       || | ||   ||||    ||   || |   |  |   | | |  |||   ||||  |  ||  |                       
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttgaatttgattattcatcaccacttgaattgccactcttaggttatt--atgacaagtttaatttgatcgagcctctttttggacaatgcag

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|58659884|gb|CK048564.1|CK048564
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAAGGCGTGGAAAGTTTGATGAATC
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAA-GGCGTGGAAAGTTTGATGAATC
EST: gi|58686263|gb|CK074950.1|CK074950
EST:     GGTGCTGAAA-TC-TGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: GGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|58672850|gb|CK061536.1|CK061536
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTG
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTG
EST: gi|571922|gb|D41433.1|D41433
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|88574877|gb|CI666646.1|CI666646
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGAAAAGCCTAAGGGGTGGAAAGTCTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|33691058|gb|CF319297.1|CF319297
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|571926|gb|D41437.1|D41437
EST:     GGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGGTGCCT                         GCACTAAACATATTTGAGACAAGNCTAAGGCGTGGAAAGTTTGATGAATC
genomic: GGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGG-TGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATC
EST: gi|58679709|gb|CK068396.1|CK068396
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|58656775|gb|CK045455.1|CK045455
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA

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: 62 (upstream exon), 56 (downstream exon)
Score: 50

GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT