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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag

Basic information

species Oryza sativa
transcript LOC_Os03g09250.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G392513_T02 (Zea mays), 5'ss of exon 4
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagctttt----cgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||||| || ||| | ||||| |||||||||||||||||||||||||||| |   ||  || ||| |   |  |   | ||      |  ||     | ||  || ||| |   ||  || ||  |||| |    |||  || || | |                
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacggcatacttacaataa--ttcttgcatatgttcattga-gagcacctag----------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacc--atatatcaaatcctttg-gctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
||| || ||||||||| ||||||||||||| || ||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||||||||||||   ||||   ||| ||   ||  ||  | |    | |    |||  |  | ||  || || |   |||| || | ||| |  |   | ||                          
TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaat-gacgttattgcaataactcttctatattttcattttcatgcag----------------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagctttt----cgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||||| || ||| |||||||||| || |||||||||||||||||||||| |   ||  || ||| |   |  |   | ||      |  ||     | ||| || ||| |   || |  | | ||| |  |  | |                            
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag----------------------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G145638_T02 (Zea mays), 5'ss of exon 2
-TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagctttt----cgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
 ||| ||||||||||||||||| |||| ||| || ||||||||||| ||||| |||||||| || ||| ||||||||||||| ||||||||| |||||||||||| |   ||  || ||| |   |  |   | ||      |  ||     | ||  || ||| |   || | || | ||| |  |  | |                            
CTATCAAGAACAACTGCCTGATCGGTGTTGACGACTTCAAGAGTGG-CAGACCAAGATGAAATCAGTCCTGGTTGATTTCCTTGTTGGTGCTAGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgtcatacttacaataattcttgtatatgttcatgcag----------------------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G02210.3 (Glycine max), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtac--caaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag------------------------------------------------
 ||   ||  |||    |||||||||| ||||| ||||||||||| ||||| || ||||| ||||| ||||||||||| || || || ||||| || |||||||        ||||  ||   | |    | | | ||    ||   | | | || |       | |    | |||| || | ||  |    |      | | |||   | ||  |                                                 
CATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgca----tgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacag

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtacc-aaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
 || ||||  |||||| |||| ||||||||||| ||||||||||| ||||| ||||||||||||||| | || |||||||| ||||| || ||||| || ||||  || | || || || |    |   ||  |||     || | | |   |  ||        || ||  ||  || |||       ||                         
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaat-aagtatcctaattaaatttat---tttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag----------------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 4
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
|||   ||| || ||  |||||||||| ||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||||| ||||| || ||||||  |       || |||       ||| | || ||   |   |||    |  | ||||      ||| | ||  |  |  | || | ||    ||| |     |         
TATATCGAAGAATTGTTTGATTGGTGGGGATGATTTCAAGAGTGGTCAGACTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAGgtaataga-----attaaa-------gcttgtttatcaagt---aac-ctaacttgcttct-----cttctgttagtgaaggaactaagaatggattttgtggcag---------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaactttt-ttttatatataacctgataagaactttggcttttgttttcgtag
 || | ||||||     |||| ||||| ||||||||||||||||| || || |||||||| |||||||||||||||||||||||||| || ||||| |||||       |  |  |  |||   |  ||   | ||   | |||||     |||||  ||   | |||||  ||| ||  ||    || |      | | |               
GATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGTTGGCGCAGGAATCAAGgt-ttgtttaacttgcgtatcaagttactctttcttgttactgaaa-----atatttgtcacaagactttggtttcattgattgtgtgtttttgtttatag---------------

upper sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ37320 (Selaginella moellendorffii), 5'ss of exon 6
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
| |  ||||       || || ||||| ||||||||||||  |||||| ||||||||||| || ||  | || |||||||| || |||||||| || ||||||        | |||   |  ||    ||  ||| ||  |  |||      |  |||||| |                                                    
TGTGGAGAAAGGAACTCTCATCGGTGGCGATGATTTCAAGTCTGGACAAACAAAGATGAAATCCGTGCTCGTGGATTTCCTGGTCGGTGCTGGCATCAAGgta--------aaatctcgtttttctcgtatttttccgactctaaatccgtcttgtcttccag----------------------------------------------------

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|218495019|gb|FG965569.1|FG965569
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|58685454|gb|CK074141.1|CK074141
EST:     AAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: AAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|3760166|gb|C97424.1|C97424
EST:     AAAGATGAAGTCTGTCTTGGTTGGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: AAAGATGAAGTCTGTCTTGGTTG-ATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|11443012|gb|BF430899.1|BF430899
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|218494828|gb|FG945589.1|FG945589
EST:     CAAAGATCAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|29686334|gb|CB682609.1|CB682609
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|58660358|gb|CK049038.1|CK049038
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCA
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCA
EST: gi|163929263|gb|EG711024.1|EG711024
EST:     AGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: AGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|218504141|gb|FG945017.1|FG945017
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|2312304|gb|C28459.1|C28459
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|218485553|gb|FG949786.1|FG949786
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|58657984|gb|CK046664.1|CK046664
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
EST: gi|218487632|gb|FG964358.1|FG964358
EST:     CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAG                         CCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC
genomic: CAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaacca ... gttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA