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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaaaacatgacatgagtttaagtttactgaactcacacactgatcatccgagggtactgacagtgtttcctttacgattttcttttactatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68380.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G166873_T01 (Zea mays), 3'ss of exon 7
gcaaaaaacatgacatgagtttaagtttactgaactcacacactgatcatccgagggtactgacagtgtttcctttacgattttcttttac---tatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG
   ||    |  | |   ||   |   |||||| | ||   | | | | |||  |  |  | | |   |||    |||  ||| ||  ||     ||   |||||||||||||||||||||||| ||||||||||| |||||||||||||||||  | |||||||||||||
---aacttaaaaaaacatgtcagaaactactgagcacatgtatttagcttccaggtattgtaataaattttttgctactttttcctactataatcatttgcagGCGCAAAGTTTCTAGTCTAGAAAAGGAGCGTCAGCATCTTCAATCTACTGTCAAAGCTCTTCAAGAAG

upper sequence: LOC_Os01g68380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G401050_T03 (Zea mays), 3'ss of exon 7
gcaaaaaacatgacatgagtttaagtttactgaactcacacactgatcatccgagggtactgacagtgtttcctttacgatttt--cttttactatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG
   ||| |  | | || |||   |   |||| |||  |   | ||    |||     |  | | |   ||| |  ||   |||   || | |  ||   |||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| |||||||||||||
--caaacatgtcatattagtcagaaactactaaacagatgaattggatttccagatattataatatatttttcgctattttttctactataatcatctgcagGCGCAAAGTTTCTAGTCTAGAAAAGGAGCGCCAGCATCTTCAATCCACTGTTGAAGCTCTTCAAGAAG
















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|29670330|gb|CB666605.1|CB666605
EST:     AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAG                         GCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
genomic: AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAGgtgaggtttt ... ctatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
EST: gi|29668085|gb|CB664360.1|CB664360
EST:     AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAG                         GCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
genomic: AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAGgtgaggtttt ... ctatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
EST: gi|125863358|gb|EL586677.1|EL586677
EST:     AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAG                         GCGCAAAGTTTCTAGTCTA
genomic: AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAGgtgaggtttt ... ctatgcacagGCGCAAAGTTTCTAGTCTA
EST: gi|58681164|gb|CK069851.1|CK069851
EST:     AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAG                         GCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
genomic: AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAGgtgaggtttt ... ctatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
EST: gi|29668122|gb|CB664397.1|CB664397
EST:     AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAG                         GCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT
genomic: AAGCTTGAAAAGGAAATTGAGGGTTTGAGCTCTGAGATTTCTTCATACAGgtgaggtttt ... ctatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatccgagggtactgacagtgtttcctttacgattttcttttactatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG
            tactgac  putative branch site (score: 1)
                                   ttttcttttactat  putative PPT
                                  attttcttttactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaaaacatgacatgagtttaagtttactgaactcacacactgatcatccgagggtactgacagtgtttcctttacgattttcttttactatgcacagGCGCAAAGTTTCTAGTCTAGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG