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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgctgtagcttatctttatctttactatttaatccctaccatgtgaaaatttacatataaactacatattatatatcttagtgtttcttttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATGATAACCAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 5
cctgctgtagcttatctttatctttactatttaatccc---taccatgtgaaaatttacatataaacta-catattatatatcttagtgtttcttttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATGATAACCAGAAAG
     | |   |||||||||| || | ||||||   ||   | ||||||||| ||||| | ||    || |  | | | | |||   | ||| |     | ||||||||||| |||||||||||| ||||||||||||||||||| ||||| ||||||||| |||||
----ttcttttttatctttattttgagtatttatcaccatgtgccatgtgaagatttatacatcgtgtagctcaatgtttctctctttttttttcgcactgcagCCTGTTGGGGTAGTTGGAGCTATTACACCATGGAATTTTCCATTAGCAATGATAACCCGAAAG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 6
cctgctgtagcttatctttatctttactatttaatccc---taccatgtgaaaatttacatataaactacatattatatatcttagtgtttcttttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATGATAACCAGAAAG
       |    ||| | | | || | |||||| | ||   | ||||||| | ||||||| |  | |||  |   |  |  ||   | ||  ||    | ||||||||||| |||||||||||| ||||||||||||||||||| ||||| ||||||||| | |||
--catcattttctatttctcttttgagtatttattaccatgtgccatgtggagatttacaaaccatctatct-caacgttgctcttttttgtttgcactgcagCCTGTTGGGGTAGTTGGAGCTATTACACCATGGAATTTTCCATTAGCAATGATAACCCGGAAG
















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|218496520|gb|FG947906.1|FG947906
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|7404226|gb|AU062684.2|AU062684
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|33794852|gb|CF323305.1|CF323305
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     ATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAG                         CCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG
genomic: ATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGGTTTTGAAGCAGgtaatatgct ... tttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaatttacatataaactacatattatatatcttagtgtttcttttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATGATAACCAGAAAG
                                        tttcttttgtt  CT-rich tract
     atttacatataaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgctgtagcttatctttatctttactatttaatccctaccatgtgaaaatttacatataaactacatattatatatcttagtgtttcttttgttacagCCTGTTGGAGTAGTTGGAGCTGTTACACCATGGAATTTTCCTTTAGCGATGATAACCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA