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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcaattgagtcagagtgcaaaccgatcatttttgcgtgtttgtgagaaatatttccaataatatctagaatagaggaagtaactttgcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os03g44900.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 6
gtatgatcaattgagtcagagtgcaaaccgat--catttttgcgtgtttgtgagaaatat---ttccaataatatctagaatag-aggaagtaactttgcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG
||| || ||  |   |   | | || ||| ||   | ||||     ||| |    ||  |   || |  |||| | ||   | | | ||||| | ||||||| || |||||||||||||||  ||||| ||  | ||||||||||| |||||||||||||||||||| ||  | ||||||||||||||||||||||||||||||||||
gtaagaacagctatattc-attccataccaatactacttttattattttttattgaacttgtttttctgtaatttgtatggttgtaagaagtgattttgcatgattagGTACATTTAGAGACGTCTATTACGAGACATAAAGCTCATATAAAGAAATTGGAGTCAATCTTGCGGCTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G340749_T01 (Zea mays), 3'ss of exon 3
gtatgatcaattgagtcagagtgcaaaccgatc--atttttgcg---tgtttgtgagaaatatttc--caataatatctagaatagaggaagtaactttgcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG
||| || ||  ||  |   | | || ||  |||   ||||| |    | ||| ||  |  | |||   | ||||| | ||    | | ||||| | ||||||| || |||||||||||||||| ||||| ||  | ||||||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||
gtaagaacagctgcattc-attccatactaatcctgtttttactatttatttatggaacttgttttttctataatttgtactgcataagaagtgattttgcatgattagGTACATTTAGAGAAGTCTATTACGAGACATAAAGCTCATATAAAGAAATTGGAGTCAATCTTGAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG
















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|66918088|gb|CX104936.1|CX104936
EST:     AGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG                         GTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTG
genomic: AGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTGgtatgatcaa ... gcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTG
EST: gi|29630458|gb|CB635467.1|CB635467
EST:     AGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG                         GTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTG
genomic: AGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTGgtatgatcaa ... gcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTG
EST: gi|29638285|gb|CB643294.1|CB643294
EST:     GAAGGACTTTCAATCT-TTAAAGGAAAGNAAAGAACTCCTCGATTG                         GTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATACCCAAATTG
genomic: GAAGGACTTTCAAT-TAAGAAAGGAAAGCAAAGACCTCCTCGATTGgtatgatcaa ... gcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagaaatatttccaataatatctagaatagaggaagtaactttgcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG
                                   aagtaac  putative branch site (score: 2)
     aaatatttccaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcaattgagtcagagtgcaaaccgatcatttttgcgtgtttgtgagaaatatttccaataatatctagaatagaggaagtaactttgcatcatcagGTACATTTAGAGAAATCTATCACACGGCATAAAGCTCACATAAAGAAATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG