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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttattcagctcttcattgtcattcctgaaaatggaaatctttaaaatggacactcctggaaaagtatgctggaataattatgtttttaatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAATTATAAAGACATCTGCTTTGCAGGTGCTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g40260.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g40260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G090715_T01 (Zea mays), 3'ss of exon 4
gtttttattcagctcttcattgtcattcctgaaaatggaaatctt-taaaatgg-----acactcctggaaaagtatgctggaataattatgt-ttttaatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAATTATAAAGACATCTGCTTTGCAGGTGCTGGAAG
      |  || |  |  ||  |   || | |||||| |    |  |  | |||     |   ||||| | || |||| |  | | |||   | ||| ||| || ||||||||| ||||||  ||||||| |||||||| |||||||| ||||||| |||||| || |||||||||||||||||| ||||
-----aaaccaccagtatatc-ttgctcttaaaaatgaatcggtggtggactggtggttatgttcctgaagaaatatgttt-actgattccatgtttcaattgacagGTGACAAGTAAAGTGCATTCTCTCAAGAAAATTCGTGGCCCTGATCCAAGTTATAAGGATATCTGCTTTGCAGGTGCTCGAAG

upper sequence: LOC_Os07g40260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G17990.1 (Glycine max), 3'ss of exon 4
gtttttattcagctcttcattgtcattcctgaaaatggaaatctttaaaatggacactcctggaaaagtatgctggaataattatgtttttaatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAATTATAAAGACATCTGCTTTGCAGGTGCTGGAAG
  |  | |  ||    |  || |  |    | |||     | |   ||| || |   |  ||      |      || ||  ||  | |||  |    || |    ||  || |  | ||||| ||||||||| |||| ||||||||||||||||| || || || ||| | |||||||||| 
catcatttaaagtgtattctttttttcaaggcaaagttttagcgacaaattgtattttattgacttgatgactctgattatgtacttatttggtttgcagATTGTGAAGGAACTTCAATCTCTCAAGAAAATCAGTGGTCCAGATCCAAATTATAATGATATATGTTTTTCTGGTGCTGGAAT
















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|33801360|gb|CF326551.1|CF326551
EST:     CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCT                         GTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT
genomic: CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCTgtaagttatc ... taatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT
EST: gi|86596688|gb|CI286601.1|CI286601
EST:     CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCT                         GTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT
genomic: CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCTgtaagttatc ... taatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT
EST: gi|58611100|gb|CK038812.1|CK038812
EST:     CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCT                         GTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT
genomic: CCACATATGCTTACCTGCCTGAACAAGCATTTGTTGCATTTAAAGATGCTgtaagttatc ... taatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatggacactcctggaaaagtatgctggaataattatgtttttaatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAATTATAAAGACATCTGCTTTGCAGGTGCTGGAAG
                                          ttttaat  putative branch site (score: 3)
                                       tgttttt  CT-rich tract
                               aataattatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttattcagctcttcattgtcattcctgaaaatggaaatctttaaaatggacactcctggaaaagtatgctggaataattatgtttttaatggatagGTGACAAATAAAGTAAATTCTCTGAAGAAAATCCGTGGCCCAGATCCAAATTATAAAGACATCTGCTTTGCAGGTGCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - -ttcagct
- - - - - - - - - - - -cattcct
- - - - - - - - - - - - - - - - -aatggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgtt