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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcagagactggaccatatgctccagtacgtaggtagtgatagtctttcttcatgtaacttctggaagtttgacatctggatcatttag

Basic information

species Oryza sativa
transcript LOC_Os01g50616.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G157043_T01 (Zea mays), 5'ss of exon 3
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagc----------agagactggaccatatgctccagtacgtaggtagtg--atagtctttcttcatgtaacttctggaagtttgacatctggatcatttag
||||||||||||  |||||||| ||||||| |||||||||||||||||||| || |||||||||||||||||||| || || |||||||| |||||||||||||          | | ||   | ||||| | |||  |  || ||||||  ||  | | | ||| | ||| || |  |||| |   |||||| || |||||
GTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAGgtaaagctaattttgtaatataccaaaacatataccccatgatatatgtagtgtgatcatttcttttcgtttaa-ttttaaaagtcta--atctgg-tcctttag

upper sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACAT---AGAGgtaaa-----gcagagactggaccatatgctccagt---acgtaggtagtgatagtctttcttcat-gtaac-ttctggaagtttgacatctggatcat---ttag
||||||||||||| | || ||||||||||| | |||||| ||||||||| | || |||||   ||||||||||||||| ||  ||||||  ||    ||||||||       |||   ||||  ||||   | ||     | |  |  ||| | |  ||| ||  | ||  | | ||    | || |  | | |    |   ||||
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag

upper sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 3
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAG---AGgtaaa-gcag----agactggaccatatgctccagtac-------gtaggt---agtgatagtctttcttcatgtaacttctggaa-gtttgacatctggatcatttag------------
 ||  |||||||| | || ||||||||||| || ||||| ||||||||| | || |||||   ||||||||||||||| || ||||| |  || |   ||||||| ||||    |   |||  ||| |  |    | |       | ||||   |||   ||     |  ||||    |  | ||  | ||| | |    |   |||              
ATTTTTGAAAGCGAGGAAGTTTGATATTGAAAAGGCAAAGCATATGTGGACTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcagttggaatttgggacatttatttggcttctgctttggcaggtttgagtacaaggaacacgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcag

upper sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G04460.1 (Glycine max), 5'ss of exon 3
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACAT---AGAGgtaaa-----gcagagactggaccatatgctccagtacgtaggtagtgatagtctttcttcatgtaacttctggaagtttgacatctggatcatttag-------------------------
||||||||||||  | || ||||||||||| | |||||| ||||||||| | || |||||   ||||||||||||||| ||  ||||||  ||    ||||||||       |||   ||||  ||||   | |  |  |||||    |   |    ||    |    ||      |||||  || || ||| | | |                         
GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgtagatagaatttggataatatttactataa--taggttacaa-gattagcctctgcggtggttggatttgtttgttat-tgcatcctctgggcttaatgttttgtgtttgcgttag

upper sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 3
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAG---AGgtaaa-gcag----agactggaccatatgctccagtac-------gtaggt---agtgatagtctttcttcatgtaacttctggaagt--ttgacatctggatcatttag------------
 ||  |||||||| | || || |||||||| || ||||||||||||||| | || |||||   ||||||||||||||| || ||||| |  ||     ||||||| ||||    |   |||  ||| || |    | |       | ||||   |||   ||        ||||    | | |  | |  ||| | |    |   ||| |            
ATTTTTGAAAGCGAGGAAGTTCGATATTGAAAAGGCAAAACATATGTGGACTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTATGCAGgtaaatgcagttggaatttggggcatttgtttggcttctgccttggcaggtttgagtacaaggaacatgacatgcttttgcagtgattggttggcttacctactgtttcgtgttttcttcag

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|58667688|gb|CK056374.1|CK056374
EST:     GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG                         GAATTTGACTATAGCGAATTAGATGAT
genomic: GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcaga ... gatcatttagGAATTTGACTATAGCGAATTAGATGAT
EST: gi|29646803|gb|CB651810.1|CB651810
EST:     GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATACAG                         GAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
genomic: GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcaga ... gatcatttagGAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
EST: gi|29625600|gb|CB630611.1|CB630611
EST:     GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG                         GAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
genomic: GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcaga ... gatcatttagGAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
EST: gi|33675178|gb|CF303417.1|CF303417
EST:     GGTCGGAAATGCTTANATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG                         GAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
genomic: GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcaga ... gatcatttagGAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
EST: gi|29663641|gb|CB659916.1|CB659916
EST:     GGTCGGAAATGCTTATATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG                         GAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT
genomic: GGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcaga ... gatcatttagGAATTTGACTATAGCGAATTAGATGATGTTCTGGAGTGCTATCCACAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAGgtaaagcagagactggaccatatgctccagtacgtaggtagtgatagtctttcttcatgtaacttctggaagtttgacatctggatcatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG