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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA

Basic information

species Oryza sativa
transcript LOC_Os12g43130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
--------------------gtacagccaacaaaaaagcta-ctgtaaaagcaggata--tgaagtgcttttaaaagttattagt-acacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
                     | || | | | |   | | | | | |  | ||   |      |   | | |  || | |   |  ||| ||     ||| ||   |||| ||         | | | |         |  |||| |   ||||| |||||||||||| |  ||||||||||||| ||||||||||| || ||||| | || ||| || |||||||||||||||||||||||||| || ||||
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctct-------ccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA

upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 3
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
                 ||  || |  ||   ||  ||      ||| || |    | |||    ||     ||  | |   || |    |||||          | | |   | ||||||    |||||| ||||| |||||||| ||||| |||||| | |||||| | || ||||| || |  | |||||||||||||||||| ||||||||||| |||||||| |
-----------------gcacctatgcaaattggtcat------cttatacag---aatagatttcaccttcttttttatgtgc-taaaactgat--ccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA

upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G41890.1 (Glycine max), 3'ss of exon 4
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagta-cacagtaaattggtgacacgcatttgtctga--tgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
                                   ||| |  | |||  |  | |||  |  |  |  |   | | || |     || ||    |  |  | |        | | |     | |||  | ||||||| || |||||||||||||| ||||||||||| ||| | || ||||| || |  ||||||||||| |||||||| ||||||||||| || || || |
------------------------------ttatgtataagttactt--agcatttagcaacaatagggggtactagttatttttatgtgctaaaactaatccaatttatactgaaatctctgtatgaatagCCATTTAAGGACATGATTGAAGGGATGAGGCTTGATCTGAGAAAGTCAAGATACAATAGCTTTGATGAACTCTACCTTTACTGCTACTATGTAGCAGGGA

upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G45270.1 (Glycine max), 3'ss of exon 3
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
          | ||  || |      |||  |   ||||||      || ||  || ||  ||     ||||   |   |           | ||| |  || |  ||      ||||||     |||||||||||| |||||||| ||||| |||||| | |||||| | || ||||| ||    | |||||||||||||||||| || |||||||| |||||||| |
----------ctaattagttctaacgaaacaaaattatgaaactagattgaaccttctttttatgtgctaaaactgaagc-----------taatgctattgaattgt------ctctttgg--aacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA

upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G13700.1 (Glycine max), 3'ss of exon 3
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagta-cacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcg---ggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
                                   ||| || | |||  |  | |||  |  |  |  |   | |  | |     || ||    |   |  | ||   ||    | ||    | | |  | ||||||| || |||||||||||||| |||||||| || ||| | || ||||| || |  | ||||||||| |||||||| ||||||||||| || |||||  
------------------------------ttatgtataaattactt--agcatttaacaacaatagggggtactacttatttttatgtgctaaaaactaatccaagttccaatgaattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG-

upper sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattgg--------tgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
                                                       || || |  || | ||     ||  | ||    ||||   | |  || |   |   ||  ||||    || ||        |  || | || | |   |   |||  ||   |    || |  ||| | | ||||| |||||||||||||| |||||||||||  | |||||| | |||||||| || |  ||||||||||||||||| || |||||||| || |||||||| |
gtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatata-aacacttccacatgttaataattttctttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGATACAACAGCTTTGATGAGCTCTATCTGTACTGCTATTATGTTGCTGGAA

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|2442819|gb|C74590.1|C74590
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGGAATGAGGGCTTGACCTGTGGAAATCAA
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGG-AATGAGG-CTTGACCTGTGGAAATCAA
EST: gi|27576401|gb|CA999095.1|CA999095
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
EST: gi|29615498|gb|CB620510.1|CB620510
EST:     ATGATGCAGGCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGT
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGT
EST: gi|29616095|gb|CB621107.1|CB621107
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
EST: gi|29615737|gb|CB620749.1|CB620749
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
EST: gi|29616097|gb|CB621109.1|CB621109
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAATG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
EST: gi|38468580|gb|CF952711.1|CF952711
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
EST: gi|58612696|gb|CK040408.1|CK040408
EST:     ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAG                         CCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG
genomic: ATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGG

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: 73 (upstream exon), 75 (downstream exon)
Score: 73

ATGGGAGAAGAGATTAGAAGATCTCTTCGAAGGCAGGCCATATGATATGTATGATGCAGCCCTCTCGGACACAGTGTCAAAGTTTCCAGTAGATATCCAGgtacagccaa ... ttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
              gtctgat  putative branch site (score: 73)
                                       tctcttttatttac  putative PPT
                                      atctcttttattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT