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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgcttcatattgtacctagtaagtcgcaagcttttttcatgataggttgattcatcttgtccatgaacctgaattatggttatcttcgcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCACCTACGAGGACAGGGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g57250.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57250.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G142768_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------ccatgcttcatattgtacctagta-agtcgcaagcttttttcatgataggttgattcatcttgtccatgaacctgaattatggttatcttcgcattt-tcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCACCTACGAGGACAGGGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTG
                                                                                               |   | | |||||    || |||  ||    | |   | |||   ||   |  |||  |   ||||||||| || |  | ||| |   | || ||||  | | ||||  | || || ||| |||||| |||  | || || ||||||||||| ||||||||||| || ||||||||||| |||||||||||||| ||
gtaagtcatatagtctgatcttttactttcactatatatatatatatatatatatatagtagaacccagttgcatacttggctatacacttaggacacgacactgtactagatatagtttcataagtctgcgaggatgttttttctgctctcatttctgaacctgatttgtactgatcgtgaaaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCACCTATGAGGACAGGGACGGGGACTGGATGCTTGTTGGAGATGTTCCCTG
















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|3760881|gb|C98135.1|C98135
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|86535627|gb|CI175833.1|CI175833
EST:     TTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACTAACTCGCTGAAACTACTAGACGACTCTGCCGAATACCAGCTCA
genomic: TTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|89170905|gb|CI040182.1|CI040182
EST:     CTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: CTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|14571418|gb|BI118786.1|BI118786
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAAGTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|58688338|gb|CK077025.1|CK077025
EST:     AGCCCTTGAAGTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAAGTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|58683213|gb|CK071900.1|CK071900
EST:     CGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAAGTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: CGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|86510796|gb|CI153429.1|CI153429
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|89176834|gb|CI013407.1|CI013407
EST:     TCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGGAAGTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: TCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|55409064|gb|CV721440.1|CV721440
EST:     GTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: GTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|87034650|gb|CI189274.1|CI189274
EST:     GGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGATACTATTAGACAACTCTGCCGAATACCAGCTCA
genomic: GGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|29645716|gb|CB650723.1|CB650723
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|89194933|gb|CI003397.1|CI003397
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACCACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|29685040|gb|CB681315.1|CB681315
EST:     AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: AGCCCTTGAACTCATGTTCACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|88979064|gb|CI025572.1|CI025572
EST:     ACGAAGCCGTCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: ACGAAGCCGTCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA
EST: gi|89198698|gb|CI003435.1|CI003435
EST:     TCCATTGGCCTTTGCGCTTCTC                         ATAATACAAACTCGCTGCAACTACTAGACAACTCTGCCGAATACCAGCTCA
genomic: TCCATTGGCCTTTGCGCTTCTCgtaagctcga ... gcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggttgattcatcttgtccatgaacctgaattatggttatcttcgcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCACCTACGAGGACAGGGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTG
  ggttgat  putative branch site (score: 5)
                                        tcttcgc  putative PPT
                           tgaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgcttcatattgtacctagtaagtcgcaagcttttttcatgataggttgattcatcttgtccatgaacctgaattatggttatcttcgcattttcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCACCTACGAGGACAGGGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG