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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatttgaacaatcatttattatcctctgtttactaatacagttattacaaatacctcagtctttaagtttcgctgacataatcttggttgaattatgtccatgctattcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGATTATAAACCTTCAACTTTGGCTGCACCTGTAGCCCCTTCTGAACTGAAGG

Basic information

species Oryza sativa
transcript LOC_Os07g22720.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 7
gtacatatttgaacaatcatttattatcctctgtttactaatacagttattacaaatacctcagtctttaagtttcgctgacataatcttggttgaattatgtccatgctattcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGATTATAAACCTTCAACTTTGGCTGCACCTGTAGCCCCTTCTGAACTGAAGG
                       |     | |  | ||||| | | | | ||    |   | || |   |  | ||  ||  |||||         |||  | |||| || ||  | |||| | |||||| |||| || |||||||||||||||||| ||||||| ||||||||||| || ||| |||  |||| ||||||||| ||| ||||||  ||||
----------------------gtacatatttactgactaa-agaataaatatggtt--ttgagacaccagttatcagtgcgataat--------gatttggcccattct-tttttcttagGTCATTGCTATAACTGTAGAAGAAGAGGGTGACATCGAGAAGTTGAAGGATTATAAGCCGTCATCTTCAGCTGAACCTGTAGCTCCTGCTGAACCAAAGG

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 3
gtacatatttgaacaatcatttattatcctctgtttactaatacagttattacaaatacctcagtctttaagtttcgctgacataatcttggttgaattatgtccatgctattcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGATTATAAACCTTCAACTTTGGCTGCACCTGTAGCCCCTTCTGAACTGAAGG
                               | |||| | |   |   | || | ||   |   ||  | |||| |   |  ||| |        ||||  | ||||||| |||   |||| | |||||| |||| ||||||||||||||||||||  ||||||||||||||||||| || ||| |||  |||| ||||||||| ||| |||||   ||||
--------------------------gtacatatttagtgac-taaagaataaatatgatttgatccatcagttaccagggtatagt--------aatttggcccatgcttttc-ccttagGTCATTGCTATAACTGTGGAAGAAGAGGGTGACATTGAGAAGTTTAAGGATTATAAGCCGTCATCTTCAGCTGAACCTGTAGCTCCTGCTGAATCAAAGG
















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|58607751|gb|CK035784.1|CK035784
EST:     TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAG                         ATTATTGCTGTAACCGTGGAAGAAGAGGGTGA
genomic: TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAGgtacatattt ... ttcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGA
EST: gi|117233831|gb|CT842341.1|CT842341
EST:     TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAG                         ATTATTGCTGTAA
genomic: TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAGgtacatattt ... ttcattttagATTATTGCTGTAA
EST: gi|58665439|gb|CK054125.1|CK054125
EST:     TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAG                         ATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGAT
genomic: TTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAGgtacatattt ... ttcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtttcgctgacataatcttggttgaattatgtccatgctattcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGATTATAAACCTTCAACTTTGGCTGCACCTGTAGCCCCTTCTGAACTGAAGG
         cgctgac  putative branch site (score: 3)
                                             ttcatttt  putative PPT
                                           tattcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatttgaacaatcatttattatcctctgtttactaatacagttattacaaatacctcagtctttaagtttcgctgacataatcttggttgaattatgtccatgctattcattttagATTATTGCTGTAACCGTGGAAGAAGAGGGTGACATCAAGAAGTTTAAGGATTATAAACCTTCAACTTTGGCTGCACCTGTAGCCCCTTCTGAACTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG