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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaaaagcatgcaaatgtgtgcagtgttgttttgctcctttttattttccccctttttgcgctcttatatttcaaattcataagccctaacttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT

Basic information

species Oryza sativa
transcript LOC_Os04g09860.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g09860.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G101250_T03 (Zea mays), 3'ss of exon 18
-gtaaaaagcatgcaaatgtgtgcagtgttgttttgctcctttttattttccccctttttgcgctcttatatttcaaattcataagccctaactt-----gtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT
    |  || ||| ||||| |||  |  |  || ||||     || ||| |||  || ||   |   ||| || || |||| |    ||| ||||     || |||||||||||||| ||||||||||||   ||||| ||||| |||||||||||||||  |||||||||||||||||| |||||||| |||||||||| |||||
taatagtaggatggaaatgagtgatgcatc-ttgtgct-----ttgtttccccttttatttatcctatatgttccatattcctggatccttactttattagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATT

upper sequence: LOC_Os04g09860.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G101250_T02 (Zea mays), 3'ss of exon 18
gtaaaaagcatgcaaatgtgtgcagtgttgttttgctcctttttattttccccctttttgcgctcttatatttcaaattcataagccctaactt-----gtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT---------------------------
                              | |||  |   ||| ||| |||  || ||   |   ||| || || |||| |    ||| ||||     || |||||||||||||| ||||||||||||   ||||| ||||| |||||||||||||||  |||||||||||||||||| |||||||| |||||||||| |||||                           
-----------------------------atcttgtgc---tttgtttccccttttatttatcctatatgttccatattcctggatccttactttattagtgcagattttgggcgtccttgatattggtaagGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATTCCTATTTTCTTCAGGCGCAAGTAATGT

upper sequence: LOC_Os04g09860.2 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv05s0049g00190.t01 (Vitis vinifera), 3'ss of exon 19
gtaaaaagcatgcaaatg-tgtgcagtgttgttttgctcctttttattttccccctttttgcgctct---tatatttcaaat--tcataagccctaacttgt-acagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT
         ||   | || |    |   ||| ||  |  |   | | | |    || ||    || |   ||| || |  ||   || |  | ||  ||  | ||||||| | ||| | |||||| ||||||||||||||||||||||||| || || |||  |   |  ||  | ||  | || ||||| ||||| |||| ||| |
-------ctatttgagtgataaaaacccttgattcaccacaagtcagtatttatctgttctgactttccatattttcctgatgaccacatcctctttctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGACTGGATTCGCAGGGGGATTCATGTTGGAAGTGGCAGAAAGTATAAGGACT

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|88490129|gb|CI427401.1|CI427401
EST:     TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTG                         ATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT
genomic: TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTGgtaagttaca ... acttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT
EST: gi|8324375|gb|AU091531.1|AU091531
EST:     TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTG                         ATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT
genomic: TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTGgtaagttaca ... acttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT
EST: gi|88516814|gb|CI442470.1|CI442470
EST:     TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTG                         ATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT
genomic: TATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTGgtaagttaca ... acttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccccctttttgcgctcttatatttcaaattcataagccctaacttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT
                                        ccctaac  putative branch site (score: 2)
                  tcttatatttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaagcatgcaaatgtgtgcagtgttgttttgctcctttttattttccccctttttgcgctcttatatttcaaattcataagccctaacttgtacagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA