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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG

Basic information

species Oryza sativa
transcript LOC_Os06g07090.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G017421_T01 (Zea mays), 3'ss of exon 10
gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
|| ||| |||||| | | | |||||| | || |||||  |||  ||   |  ||||| |  | | |  ||||||||||  ||||  | ||||||||||||| |||||||| ||  | |||||||||||||| ||||| ||||||||||| |||||| || ||||| | ||||| |||||||| ||||||
gtgtggcgaaataataaat-ttctttgtaatgtatactgttggatt---atatatctaatgtgcatatatctcttctatgttgatatgtttagGAAAGTTTAGTTAGGGTGGCCATTTGGTGCATTGGTGAATATGGAGAAATGCTGGTCAACAATCTTAGTATGTTAGACATGGAGGAACCGATCACG

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------------------------------------gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
                                                                                                   || |||||||||| | | | |||||| | || |||||  |||  ||   |  ||||| |  | | |  ||||||||||  ||||  ||||||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||||||||||| |||||| || ||||| ||||||| ||||||||||| |||
gtatggcatgctcttatagttctagtgagtaatgcatctgaacttcaaggatattcagtcaggtcattatataaagcattgcaagcatctagtgaacaggtgtggagaaataataaatgttctttgtcatgtatactcttggatt---atgtatctaatgtgcatagatctcttctatgttgatatatttagGAAAGTTTAGTTAGGGTGGCTGTTTGGTGCATCGGTGAATATGGAGAAATGCTGGTCAACAATCTTAGTATGTTGGACATGGAGGAACCAATTACG

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G030144_T02 (Zea mays), 3'ss of exon 9
gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
|| |||||||||| | | | |||||| | || |||||  |||  ||   |  ||||| |  | | |  ||||||||||  ||||  ||||||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||||||||||| |||||| || ||||| ||||||| ||||||||||| |||
gtgtggagaaataataaatgttctttgtcatgtatactcttggatt---atgtatctaatgtgcatagatctcttctatgttgatatatttagGAAAGTTTAGTTAGGGTGGCTGTTTGGTGCATCGGTGAATATGGAGAAATGCTGGTCAACAATCTTAGTATGTTGGACATGGAGGAACCAATTACG

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 10
gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
||    |    |  |  | |    |   |    | ||  || | |||||  | ||       |  | ||| |   ||| |||   ||  | |||| | | | ||| | ||  | || ||||||||||| ||||||||||| ||| | || || |||||||| ||||| |||||||| || ||||| || 
gtgctcacttctgctttgaccaaatctagg--cacactgttaatttgcttttgatgcctttcatat-aatattaccta-attcttttcatcagGAGACTCTAGTTCGAGTTACAGTGTGGTGCATTGGGGAGTATGGTGACATGTTAGTTAATAATGTTGGAATGCTTGACATAGAAGATCCAATAACA

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 9
gtatggagaaatagtcagtcttctttatgatcta----taccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
            | |    |||    |  |||||     |   || | |||||  | ||       |  | |   |     | | |   ||  | |||| | | | ||| | ||  | || ||||||||||| ||||||||||| ||| | || || |||||||| ||||| |||||||| || ||||| || 
------gtgctcacttctgctttgacaaaatctaggcacattgttaatttgcttttgatgcctttcatataatattacctaatactt--ttcatcagGAGACTCTAGTTCGAGTTACAGTGTGGTGCATTGGGGAGTATGGTGACATGTTAGTCAATAATGTTGGAATGCTAGACATAGAAGATCCAATAACA

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
-----gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgaca--tacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
      | ||     ||   || |   |  ||   |||      |    |      || ||| ||   | | |  |    |  |    |   ||  | ||||| |  | ||  | || || || ||||||||||| || |||||||||||| | || || |||||||| ||||| || ||||||||||| || || 
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT

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|58654587|gb|CK043267.1|CK043267
EST:     GATACTCAGTGAGATCATTATACAAGGCATTGCTAGCTTGCGGTGAACAG                         GAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAAT
genomic: GATACTCAGTGAGATCATTATACAAGGCATTGCTAGCTTGCGGTGAACAGgtatggagaa ... aattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAAT
EST: gi|58673720|gb|CK062406.1|CK062406
EST:     GATACTCAGTGAGATCATTATACAAGGCATTGCTAGCTTGCGGTGAACAG                         GAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATG
genomic: GATACTCAGTGAGATCATTATACAAGGCATTGCTAGCTTGCGGTGAACAGgtatggagaa ... aattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG
               atctgac  putative branch site (score: 3)
                                      tacattgaattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgacatacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA