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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgaagaatatttgtgcctttatgagataactatttgctctcaattacaatatgtttatttgcttatccccccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA

Basic information

species Oryza sativa
transcript LOC_Os06g02550.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02550.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 10
gtgagtgaagaatatttgtgcctttatg--------agataactatttgctctcaattacaatatgtttatttgcttatccccccgttc-cagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA
|| |||||| ||||| |||| ||||||         ||| |   | ||| |  || ||     || | |||||| ||     |   ||  |||| |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||| |||| 
gtaagtgaaaaatatctgtggctttatctgaataccagagagtgaattgatgccatttcattaatatatatttgtttcctatcatattttcagACATGTGGGCAATGGGTGCCATTATCGCGGAGCTATTTTCACTGCGACCTCTTTTTCCTGGATCAAG

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------gtgagtgaagaatatttgtgcctttatgagataactatttgctctcaattacaatatgtttatttgcttatccccccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA
              |     || || |   ||  |||| | |||||      |||  |   | |||||   |   |||  || |      ||| |||||||||||||||||||||| || || |||||||| || || || || ||||| || |||||  | | 
gttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgt------gtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
















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|58674281|gb|CK062967.1|CK062967
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         AATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagA-TATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTC
EST: gi|58655521|gb|CK044201.1|CK044201
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGA
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGA
EST: gi|58662294|gb|CK050974.1|CK050974
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|29641486|gb|CB646493.1|CB646493
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|58687727|gb|CK076414.1|CK076414
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|58677581|gb|CK066268.1|CK066268
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|58657844|gb|CK046524.1|CK046524
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGANCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|29658028|gb|CB654303.1|CB654303
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCCTCATCGCCGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|58685041|gb|CK073728.1|CK073728
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|29685601|gb|CB681876.1|CB681876
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
EST: gi|58689016|gb|CK077703.1|CK077703
EST:     CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG                         ATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC
genomic: CCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTGgtgagtgaag ... cccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataactatttgctctcaattacaatatgtttatttgcttatccccccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA
 agataac  putative branch site (score: 3)
                                     cttatccccccgttcc  putative PPT
               tcaattacaatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgaagaatatttgtgcctttatgagataactatttgctctcaattacaatatgtttatttgcttatccccccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT