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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctaaacacgttcaggttgcactcttttcgtgctcagcctattatttttcttgattgcttaatttttggcacctcagttatgaaactactacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCTTTCTCCAAGATGGTTCAGAGTACAGGACCTAGCAATGCAGAGTACCTGA

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 25
agctaaacacgttcaggttgcactcttttcgtgctcagcctattatttttcttgattgcttaatttttggcacctcagttatgaaactact-----acttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCTTTCTCCAAGATGGTTCAGAGTACAGGACCTAGCAATGCAGAGTACCTGA
       |    | | ||  || || | | || |    | || | ||| |  ||   | |||||  |       ||| |  ||| |  |||        ||||||||| |||| ||||||||||||||||||||| | ||||| |||   |||||||||||||||||||| || ||||||||||||||||| ||||| ||||| |
-----ttctttgtaatgtcacattcatgttgtacaggtcttaatgtttgttgtgtaagattaatcgtgatattttcactagtgagataactttggagtatttcagGTTCTGGAATTCGACTCTCCTGAGAATCTTCTAAGCAACGAGGGGAGTGCTTTCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCA
















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|58655688|gb|CK044368.1|CK044368
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|33380305|gb|CF195648.1|CF195648
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGANN                         NTTTTGGAGTTCGACTCTCCTGNNNATCTTTTGAACAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|33685919|gb|CF314158.1|CF314158
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|112787004|gb|EE591866.1|EE591866
EST:     GACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: GACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|88354423|gb|CI624813.1|CI624813
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|58693939|gb|CK082626.1|CK082626
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|58658993|gb|CK047673.1|CK047673
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATC
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATC
EST: gi|33380452|gb|CF195795.1|CF195795
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAACAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|33380456|gb|CF195799.1|CF195799
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAACAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|33380394|gb|CF195737.1|CF195737
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAACAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|58657519|gb|CK046199.1|CK046199
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|66919516|gb|CX106364.1|CX106364
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|38481628|gb|CF965717.1|CF965717
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|38477879|gb|CF962012.1|CF962012
EST:     CTAAGTGCTGGG-AG                         G-TTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: CTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttgattgcttaatttttggcacctcagttatgaaactactacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCTTTCTCCAAGATGGTTCAGAGTACAGGACCTAGCAATGCAGAGTACCTGA
            gcttaat  putative branch site (score: 4)
                                            ctacttttc  putative PPT
         attgcttaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctaaacacgttcaggttgcactcttttcgtgctcagcctattatttttcttgattgcttaatttttggcacctcagttatgaaactactacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCTTTCTCCAAGATGGTTCAGAGTACAGGACCTAGCAATGCAGAGTACCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG