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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaactagaccaaattatcaggttgcatatgttattgtggctctcctttctatgatgggttttgcttcattagattaaaaatgaaaactgtttaacctatgcataacggctttcttctctaccccattcag

Basic information

species Oryza sativa
transcript LOC_Os02g43350.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 11
CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaactagaccaaattatcaggttgcatatgttattgtggctctcctttctatgatgggttttgcttcattagattaaaaatgaaaactgtttaacctatg---cataacggctttcttctctaccccattcag
 ||||||||||||| ||| | ||  | || || || || |||||||||||| | |||||||||||| |||||||||||||||| |||||||||||||||||| |       | ||||    |  |    | ||||||||   || ||| ||   | | ||  | ||||| ||||||| | ||| || |||| ||||| |  | ||     ||||  |||  ||   | |     ||||
AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtga----tctgcccaatgatttggacgacttatgttat---ggttctgctagatgtcatttgatttgcctcattaggt-aaacataaaaattgttttatgtgtggtgtgtaacttcttgttttcatgcgttgatcag

upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 12
CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaactagaccaaattatcaggttgcatatgttattgtggctctcctttctatgatgggttttgcttcattagattaaaaatgaaaactgtttaacctatgcataacggctttcttctctaccccattcag
 ||||||||||||| ||| | || ||  | || || || |||||||||||| | |||||||||||| |||||||||||||||| |||||||| ||||||||| |     |   || ||| |||  | ||| | | | ||  ||| ||| || | |   ||     ||  |||||    |      | |   ||  ||  | |     |  | |                      
AGGGAAGTAAAAGCGCTTTTACAGTCGTCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATACTTAGAAGgtga-----tcagcccaatgatcttgatgcct-tatgat-atggttctgctatatgccataaaagttatttcat-gtgtggtgtgtaacttctcgttgtcatgcatttttcag----------------------
















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|29687896|gb|CB684171.1|CB684171
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGANAAGGTTGAGGGCGAGGAGCTTCA
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCA
EST: gi|29674692|gb|CB670967.1|CB670967
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|427407|gb|D23472.1|D23472
EST:     GCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: GCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|88231248|gb|CI231097.1|CI231097
EST:     CCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATG-AAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: CCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|88220696|gb|CI220256.1|CI220256
EST:     CTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: CTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|29687897|gb|CB684172.1|CB684172
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|29630419|gb|CB635428.1|CB635428
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|86827098|gb|CI270817.1|CI270817
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTAG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|33800967|gb|CF326357.1|CF326357
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|86436764|gb|CI118486.1|CI118486
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|29625158|gb|CB630169.1|CB630169
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|29630417|gb|CB635426.1|CB635426
EST:     TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: TGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
EST: gi|427516|gb|D23583.1|D23583
EST:     ATATTTAGAAG                         AGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG
genomic: ATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 54 (downstream exon)
Score: 26

CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaact ... ccccattcagAGAATGAAAAGGTTGAGGGCGAGGAGCTTCAAGAGTGGCTCAAGTCGGTTGTTGCACCAAAAGAATTGACCTCATTTATAAGAGGAAAGCAAGAGCAGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaactagaccaaattatcaggttgcatatgttattgtggctctcctttctatgatgggttttgcttcattagattaaaaatgaaaactgtttaacctatgcataacggctttcttctctaccccattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA