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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgctataatgtggtgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g44000.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgtta---tta-----tatataactaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgctataatgtggtgtttgcag
|||| |||||||| || |||||||| || ||||| || || || ||||| ||||| ||  |||| |||||||| ||||| ||||||||||| |   |||      |||  |||    |  |||  |  |   | | || ||   | |    | |   || || |||| |||||  |||||||||
ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccata-gccagactctaactagctagaatgtattgtttgcag

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacacccttcccattttctttcgctgaccaaaa------acattaaaaggtatcttgcta-------taatgtggtgtttgcag-------------
|||| || ||||| || |||||||| |||||||| || | ||| ||||||||||||||| | || ||| | ||||||||||| ||||||||| ||   | |   |       || || | ||     | |  |||||         ||||  |||| |    |||        |||||| | |||                 
ATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAGgttctttcttcttcttcgtg---tttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcag

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataa-ctaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgc------tataatgtggtgtttgcag------------
|||| |||||||| || ||||| || |||||||| || ||||| ||||||||||||||  | |||||| | |||||||| || | |||||||  || || | | ||  ||| |||   ||| | | || |  |   |||   ||  |   |  |   |      ||  ||||  | ||  |              
ATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAGgtttctacatttgatctctcacactttgtattgt-tgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcag

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatata------actaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgctataatgtggtgtttgcag--------
||||  |||||||||||||||| || || ||||| || |||||  |||||||||||||| | || ||| | ||||| ||| | |  |||||| || |  ||       |||| |||  |||  ||  |  |  | | || |   |  ||        |  |||||| ||    |  |    |        
ATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtccatctttcttactagcact-ttcatatccttctcggttcacaattcaacttggttttccttgtgctatgattcaattctctggggcaaagct

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacac-----ccttcccatttt---ctttcgctg-accaaaaacattaaaaggtatc-ttgctataatgtggtgtttgcag----
|||| || ||||| ||||||||||| |||||||| || |||||  |||||||||||||  |||| |||||||| |||||| | |  ||||| | | | || |  |  |||     ||| | | | ||    ||||  |  | |  |   |  ||  || |   ||  | || |||  || || |      
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgt-actttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacacccttcccattttctttcgctgaccaaaaaca------ttaaaaggtatcttgct--ataatgtggtgtt-tgcag-----
||||| ||||||| ||||||||||| ||||||||||| || ||  |||||||||||||  | || ||||| || |||||| |||  ||||| ||  | |  | || |     ||| ||  ||   ||  ||   | |||        | || |  ||     ||  || |  | || || ||  |     
ATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAGgt-atcctgttaacctgaacttgttcacacgtttaatctttggatagaaaagcgcgagtaaagaaatactacacttaatgacattgttttatgttgacttc

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|88536811|gb|CI464600.1|CI464600
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88661438|gb|CI455114.1|CI455114
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88547046|gb|CI477317.1|CI477317
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTNCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|163920049|gb|EG709843.1|EG709843
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|13896698|gb|AU183034.1|AU183034
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88555102|gb|CI485335.1|CI485335
EST:     GTTCGGTGTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|8857593|gb|AU094911.1|AU094911
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88541762|gb|CI471050.1|CI471050
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88375124|gb|CI523389.1|CI523389
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|58593809|gb|CF992117.1|CF992117
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGGTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88521140|gb|CI448799.1|CI448799
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88237642|gb|CI237491.1|CI237491
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAACGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88661342|gb|CI452697.1|CI452697
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88466336|gb|CI529745.1|CI529745
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88536272|gb|CI466013.1|CI466013
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|8857008|gb|AU094326.1|AU094326
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88528856|gb|CI457128.1|CI457128
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|86822411|gb|CI357963.1|CI357963
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGC-AAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|5851049|gb|AU078221.1|AU078221
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|8856902|gb|AU094220.1|AU094220
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|88549272|gb|CI479148.1|CI479148
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
EST: gi|86888775|gb|CI307833.1|CI307833
EST:     GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG                         CAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG
genomic: GTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatat ... gtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgctataatgtggtgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG