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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagtgctcttttacgtaagtgtgctggctgagcgcctttgagattcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g15780.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G161337_T03 (Zea mays), 3'ss of exon 1
tgtagtgctcttttac-gtaagtgtgc-tggctgagcgcctttgagattcttgtcttctgtacttacactgaaaaacaatg-tattgt-ttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
     ||   ||| |   | ||||| | |||  ||      | |   ||      |  || | |  ||   |||||   |   || |  ||||||| ||| ||||| |||||| ||||||||||||||||||| |||||||||||| || |||| || ||||| ||||||||||| ||||| |||||||||
---gatggattttgattattagtgtacatggtagaagattctaggctttggaaaatattgcaatgtcatgcaaaaattgtaacatcgggttgaatg-tttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 9
-tgtagtgctcttttacgtaagt-----gtgctggctgagcgcct----ttgagattcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
 || ||  |  |||   || |||     ||| | | ||     ||    | || | | ||   ||   |  ||    |  |||| ||  | ||| ||  ||   ||  |||| | |||||||||| | |||||| |    || ||||||||||||||||| || |||||||||||||| || |||||||| ||||||
gtg-agaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgatt--atttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA18G03270.1 (Glycine max), 3'ss of exon 8
--tgtagtgctcttttacgtaagtgtgctggctgagcgcctttgagattcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
     |      | || |   |      |   | ||  |  | |  ||| ||   ||   |  ||    | ||| | ||  | ||| ||  ||   ||  |||| | |||||||||| | || ||| |    || ||||||||||||||||| || ||||| |||||||| || |||||||||||||||
gtcccaaaaaattatttctctatccaattaagtcagaacactgggtattatttcattgcatttttctgtttaaacaaaaaatgttgctt--atttattgtagGTTACTGGAGAGTTGCAAGAGCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCCGTTGGAACTGTCAGTGGAGCACCAAAG

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------------------------tgtagtgctcttttacgtaa-gtgtgctggctgagcgcctttgagattcttgtcttctgtacttac--actgaaaaacaatgtattgtttgaatga-tttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
                                                             |    |  | |   | | || |  ||||||   | |   ||  || || || |    | ||   ||  | | |  |  |||  | |  || |  |  ||| ||||| | |||||| ||   ||||||| |    || |||||||| || || || || ||||||||||||||||||||||| |||||||||
gtaaatataaattttgtaataatttatcaaggctgtttttacatatcatcataggatttgataacataatataaaaggcaatggatgctggagaaacatatt--agtttgttattcagtataacaactgattcattactaataaaatccttaaccggctttgcagGTTACTGGAGAATTACTTGATCATTTAACCAGCTGGGATGCTCTACGTGCTGCATTGCCTGTTGGAACAGTTAGTGGGGCACCAAAG

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|29624822|gb|CB629833.1|CB629833
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29616792|gb|CB621804.1|CB621804
EST:     CATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: CATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29616044|gb|CB621056.1|CB621056
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29662736|gb|CB659011.1|CB659011
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29646546|gb|CB651553.1|CB651553
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29662735|gb|CB659010.1|CB659010
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|25803679|gb|CA759640.1|CA759640
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGANCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29628879|gb|CB633890.1|CB633890
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
EST: gi|29614551|gb|CB619564.1|CB619564
EST:     AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG                         GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC
genomic: AATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCC

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), 75 (downstream exon)
Score: 7

GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctct ... tgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
             tacttac  putative branch site (score: 7)
                        aaaaacaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagtgctcttttacgtaagtgtgctggctgagcgcctttgagattcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA