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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattccatctaatgcaagtttccctttcatttctgggtaccatcgcttatgagttatgaagaacatttggttcatcctgattcag

Basic information

species Oryza sativa
transcript LOC_Os03g61950.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G351160_T01 (Zea mays), 5'ss of exon 5
ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattccatctaatgcaagtttccctttcat-ttctgggtaccatcgcttatgagttatgaagaacatttggttcatcctgattcag
|| ||||||||||||| ||| | || |||||||||||| |||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||  || | ||       ||||| | ||  | |  |||| ||  ||| |||       |||||  |      ||| | ||||||
ACTTATGGCAATGGTCGGAGATGACTGGCTTTGGTGATTTACCGTCACCACGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAGATTGTTATgtaagcatt--atttgatatgcacatccctgtgatactttttgtactattacttttga-------agaacgctc----tatctttattcag

upper sequence: LOC_Os03g61950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G468485_T01 (Zea mays), 5'ss of exon 3
ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattccatctaatgcaagtttccctttcatttctgggtaccatcgcttatgagttatgaagaacatttggttcatcctgattcag-----------------
|| ||||||||||||| ||| | || |||||||||||| |||| ||||| |||||||||||||||||||||||||||||||||| ||| |||||||||||||||||  || | ||       ||||| |  |       || |||||       | ||||  |       | |||||     | ||                  
ACTTATGGCAATGGTCGGAGATGACTGGCTTTGGTGATTTACCGTCACCACGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAAAAAGATTGTTATgtaagcatt--atttgatatgcacatccctgtggtac-----taacatcgtgagaatgctatggtgttgcccagtttcatttaagtccaagaagctggtgaagatgg

upper sequence: LOC_Os03g61950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G32900.1 (Glycine max), 5'ss of exon 5
ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaag---cattccatctaatgcaagtttccctttcatttctgggta-ccatcgctta---tgagttatgaagaacatttggttcatcctgattcag
| |||||||||||||| ||  |||| ||||| |||||  | || ||||| ||||| |||||||| ||||||||  | |||||| | ||||||||||||| ||    ||    | | ||   | |     ||| | | ||   || |    |  ||   | |   ||| ||     | | |||    |||| |||
ATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTATgtgaggcatatagtgtttgatttgactggtttttttaatgctaattagctgaagagtaaattaaaacatgtagtgaggtggattctgtgtgatgcag

upper sequence: LOC_Os03g61950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0074g00620.t01 (Vitis vinifera), 5'ss of exon 6
ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcatt--ccatctaatgcaagtttccctttcatttctgggtaccatcgctta---tgagttatgaagaacatttggttcatcctgattcag
| |||||||||||||||||| | ||| | ||||||||  | || |||||  | || ||||| ||||||||||| || |||||| | ||||||||||||| ||  ||    ||   || || | |   |   |   | |   |    |  | ||   ||  || | |||   | ||  || || | |      
ATATATGGCAATGGTCAGAGCTGACCAGTTTTGGTGACTTGCCTTCACCAAGGGATTTTGCAGCTGCTTCAGCTATTGGAAACCGGAAAATTGTTATgtgagtgttaataattgcatccatgatcaaccaactgatttaatttttttttcctaacttgcattctaaagctaacttatttaatgcag------

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|117250064|gb|CT843884.1|CT843884
EST:     CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTAT                         GTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA
genomic: CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattc ... cctgattcagGTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA
EST: gi|29686595|gb|CB682870.1|CB682870
EST:     CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTAT                         GTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA
genomic: CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattc ... cctgattcagGTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA
EST: gi|88361530|gb|CI605311.1|CI605311
EST:     CTCGAGAGTTTGCTGCTGCTTCAGCCATAGGGAAACAGAAAAATTGTTAT                         GTATGGCGGTTGGGATGGCAAAAAATGGTTTGTCGGATGTATACATCATGG
genomic: CTCGAGAGTTTGCTGCTGCTTCAGCCATAGG-AAACAGAAAAATTGTTATgtaagcattc ... cctgattcagGTATGGCGGTTGGGATGGCAAAAAATGGTT-GTCGGATGTATACATCATGG
EST: gi|40486394|gb|BX897943.1|BX897943
EST:     CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTAT                         GTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA
genomic: CCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattc ... cctgattcagGTATGGCGGTTGGGATGGCAAAAAATGGTTGTCGGATGTATACATCATGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTATgtaagcattccatctaatgcaagtttccctttcatttctgggtaccatcgcttatgagttatgaagaacatttggttcatcctgattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT