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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgttttatattttatagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag

Basic information

species Oryza sativa
transcript LOC_Os03g52840.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 9
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgttttatatttta--tagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag
|||||| ||||||||||| ||||||||||||||||| || |||||||||||||| || ||||| ||||||||||||||||| ||||||||||| || ||||||||   |||||   || | || ||||| ||||| |   |   ||| ||||||||||||| | |  | |||| |       || ||  || |||
GTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctccactt---attcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgt--tttatattttatagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag-------
||||||||  || ||||| |||||    ||||| ||||| || ||||||||||| || || || || || |||||||| |||||||||||| | ||||||||    |            | | || |  |   || ||||    |    |   | | |   | ||  || |  ||  |  || | | |||  | |       
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataatttgatcattactttaccagt-gtttcaatagtcacagactgaga-tggaagggatctgtgtcactgtctgtttttct

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 10
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtc-tgtagcacttctgatccctgatgttttata-ttttatagatcacatt--gtttgcctttgtcttggactc--taaaaggact-ttcta-acttccag
|||||||| ||| ||||| ||||||   |||||||| || || || |||||||||||||| |||||||| ||| |||||||||| |||||  | || |||||  | || |     |  | ||   ||   || | |||| | |||| ||||   ||      ||  || || ||  |     |||| ||||    ||  ||
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGAAACAGgttatttatctaaagtatttccaactggaatacaattttttggatctcatttcattcaaagctgattttgattcatttctttgactattctgtggttgtag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 10
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgttttatattttatag---atcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag---------
|||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | || |||||||||      ||||       |  ||| |||| |||  |   || ||||| |||   ||| | |||    | |||||||              |         
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgt----tctctggctggataattttcatatattaatgcgcattacatttttttttttttttttgtgg-caaaaaggaaagagggggggggggaagaatgaa

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 5'ss of exon 3
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgttttatattttatagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag-----------
|||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | || |||||||||      ||||       |  ||| |||| |||  |  ||     |||   ||| | || |   | |||||||              |           
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgt----tctctggctggataattttcatatattaatgcgcattacatttttttttttttttgtggcaaaaaggaaagaggggggggggggggaaaaaaga

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|58691302|gb|CK079989.1|CK079989
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38474524|gb|CF958657.1|CF958657
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38479794|gb|CF963883.1|CF963883
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29687054|gb|CB683329.1|CB683329
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|4716856|gb|AU057972.1|AU057972
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38474897|gb|CF959030.1|CF959030
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|13420583|gb|AU174673.1|AU174673
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|11442748|gb|BF430651.1|BF430651
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29675548|gb|CB671823.1|CB671823
EST:     TCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: TCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38476360|gb|CF960493.1|CF960493
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTGGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGT
EST: gi|29629705|gb|CB634714.1|CB634714
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29621679|gb|CB626690.1|CB626690
EST:     TAGCTG-TGCGCTTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTG
genomic: TAGCTGTTGCGC-TTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTG
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|33663440|gb|CF294407.1|CF294407
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38482519|gb|CF966548.1|CF966548
EST:     GCGCTT-AGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTATCTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAAGT-ATGAGTAACTG
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAA-GTTATGAGTAACTG
EST: gi|58692040|gb|CK080727.1|CK080727
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|55410185|gb|CV722561.1|CV722561
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38472677|gb|CF956809.1|CF956809
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|29674139|gb|CB670414.1|CB670414
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|55411163|gb|CV723539.1|CV723539
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|38478032|gb|CF962165.1|CF962165
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|428581|gb|D24733.1|D24733
EST:     GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGT
EST: gi|218505280|gb|FG952910.1|FG952910
EST:     GTGGACCACATAATCATACCATTACTGGCTTACCTGTTGCGCTTAAGCAG                         GCAACTACTCCGGAGTACAGAGCTTAT
genomic: GTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagca ... taacttccagGCAACTACTCCGGAGTACAGAGCTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgttttatattttatagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT