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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG

Basic information

species Oryza sativa
transcript LOC_Os03g22420.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
gtatttt---actaaatga-ttgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
||| ||    | |  |  |    || ||  |     |||  || | |||||| | | ||||| ||  |       | |||  | |||||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| |||
gtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatag-catctaaataac------ctattttc-cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 1
gtattttactaaatgattgctattagtccatggtttt-gtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
      |||| |  ||||   || || |  |  |||| |    | |||       |||    | ||    ||   |      ||||| ||||||||||| | ||  ||||||||||||| ||||||||| |||| |||| |||||||||||| ||||| ||||| |||
-----gtacttatcgattag-atgagcctctatttttaggcagtacatacattatatcatctaaataacctattttc----tagTGGCTTGGTGAAGGAAAAAA--TTGTGAAAGCTGTGTTTTCACTGACAAG-AAAAATGCTCCAAGTGTAATTTTTGTGGACGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
        |  || |||   |   |  || | |||  || | |   ||     ||      |||||     || |      || |  |||||||||||||| || || |||| ||| |||||||| ||||| ||||| || ||||||||||| || || || || || || || 
gttaaatttgcttcactgggtttattttaat-gtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
---gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
     | | |  ||||| | |  | ||  |   |  ||   | | ||| |      ||    |||||| || |    ||    ||||||||||||||||||||||| | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || || |||
gtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggt-tttgtttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 18
gtatt--ttactaaat-gattgctattagtcca---tggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
|||||  || | || |  |    | ||  || |   ||  |||  |||      |  |  |   || | ||  |||    ||    |||||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||
gtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
---gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccatt-accacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
    || | |  ||| | | |  | || ||   ||  |||  || |    ||  |  |   |||| ||   ||    ||     ||||||||||||||||||||||||| ||| |||||||| ||||| || || |||||||||||||||||||||||||| || || |||
gtattaatgttgtaagttacttttttttgtg-gtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
        |  || |||   |   |  || | |||  || | |   ||     ||      | ||| |   || |      || |  |||||||||||||| || || || |  ||||||||||| ||||| |||||||| ||||||||||| || || || || || || || 
gttagatatgcttcactgggtttattttaat-gtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 18
gtattt-tactaaatgattgctattagtccatggttttgtttttgcattttgggcatc---tga-aacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
|||||  |   ||||     || ||  | |     | ||| ||| | |||    |||    ||| |  ||  |||    ||    |||||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||
gtattagttgcaaatttaaactgttt-tgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
---------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaaca-ttgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
         || | |  |||| ||  |  |   | | ||   || |   |||||  |     || || |     |||  |    || |  |||||||||||||| || ||||| | |||||||||||| || || ||||| || |||||| | || |||||||| || || ||||||
gttaaatttgtctctctctaagtgtatattg--atttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 21
gta--ttttactaaatgat-tgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccat-taccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
|||  | | |  || |||| || | |   |  ||| |||  |||    |||    | |  |||    ||       ||      |||||||||||||| ||||||||||  || |||||||| || ||  | || ||||| ||||| |||||||| ||||| || ||||||
gtaactctcataaagtgatatgatttccttttatgctttcttttaatgatt----gtacttgaccatttacactaaatgctttgcagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
       | |    | ||||| |  ||||    |  |  |||     |    |||||   || |   ||||  || |   |     ||||||||||| ||||||||||| | ||| |||||||| || || || || || |||||||| || |||||| |||| || || |||
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctg-atattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
-----------------------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
                        | || ||     ||||  |||| |||   | ||| | ||||    ||||   || |||     |  | |  | ||    ||||||||||| || || ||||||| |||||| || || || ||||| || || ||||||||||| |||||| | || |||||||| 
gttatcattgataagtagcttcttttttctatcccttgatctctat-agtgggttgttatttttt----tttttctcagctggtttctcatctttc-ttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAA

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|58688470|gb|CK077157.1|CK077157
EST:     AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAG                         TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC
genomic: AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtattttact ... attaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC
EST: gi|58662327|gb|CK051007.1|CK051007
EST:     AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAG                         TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC
genomic: AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtattttact ... attaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG
     ttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA