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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttattatatttgttcaattttgtttttttctcctgttgatttatacctttctgtctcctgttgatttatggacaataataatgtagcatttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATCTCTG

Basic information

species Oryza sativa
transcript LOC_Os06g07090.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 8
-ctttattatatttgttcaattttgtttttttctcctgttgatttatacctttctgtctcctgttgatttatggacaataataatgtagcatttcaaat-agGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATCTCTG
|| || || | | | || || | || | | | | | | |||||| ||||||||| ||| | | | ||||| | |||||||||| || | || |||||||||||||||||||||| ||||||||||||
gaattgttttaaat-tctgtgctggtattgaaaaaataatggatcgt-tttgtttatttcctgtggatttatgggaaattaacagttgtcattttttgttagGTTTTCCCTGGACAGGCTATGGTACTTAGACCAGATGTTCAGAGTTTTATCTCTG

upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 8
ctttattatatttgttcaattttgtttttttctcctgt---tgatttataccttt--ctgtctcctgttgatttatggacaat-aataatgtagca-tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATCTCTG
|||| || |||||||| | | | | || | | ||| | | |||||| |||||||| ||| ||| | | ||| ||| ||||||||||| || || || |||||||||||||||||||||| ||||| ||||||
-------gaattttttaaattttgtgctggtattgaaaaaataatggaaaattttgtttatttcctgtctatttatgggaaattaatggtttggcactttttgttagGTTTTCCCTGGACAAGCTATGGTACTTAGACCAGATGTTCAGAGTTTTGTCTCTG
















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|29624901|gb|CB629912.1|CB629912
EST:     CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAA                         GTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
genomic: CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAAgtaagacttg ... tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
EST: gi|58654587|gb|CK043267.1|CK043267
EST:     CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAA                         GTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
genomic: CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAAgtaagacttg ... tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
EST: gi|29672354|gb|CB668629.1|CB668629
EST:     CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAA                         GTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
genomic: CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAAgtaagacttg ... tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
EST: gi|58673720|gb|CK062406.1|CK062406
EST:     CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAA                         GTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
genomic: CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAAgtaagacttg ... tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATC
EST: gi|58655701|gb|CK044381.1|CK044381
EST:     CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAA                         GTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGT
genomic: CAGGACTTCAAGGACGACCTCACAGCAAAGATATGCTCAATTGTTGAAAAgtaagacttg ... tttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctttctgtctcctgttgatttatggacaataataatgtagcatttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATCTCTG
               tgttgat  putative branch site (score: 4)
 acaataataatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttattatatttgttcaattttgtttttttctcctgttgatttatacctttctgtctcctgttgatttatggacaataataatgtagcatttcaaatagGTTTTCCCAAGATAAACTTTGGTACTTAGACCAGATGTTCAAGGTTTTATCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG