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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaagagctggtttttgcttacatgcctcccaccctggaaacttgaaaatctattttcttaactctatcatttgctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTGGACGAGAAAATCTCAGGTTGTGTGAGAGAAGTGATCTATTGCAGTTCTG

Basic information

species Oryza sativa
transcript LOC_Os01g06590.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G305901_T01 (Zea mays), 3'ss of exon 5
gta-gaagagctggtttttgcttacatgcctcccaccctggaaacttgaaaatctattttc--ttaactctatcatttgctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTGGACGAGAAAATCTCAGGTTGTGTGAGAGAAGTGATCTATTGCAGTTCTG
||| | || ||||  | |||||  ||     |   | | |||||  |||| || |  || |   |||  | ||  || | ||||  ||||||||| ||||||||||||||||||| || ||||||  |||||||||||  || |||||||| ||    || |||| ||||||| |||  |||||||| |
gtaaggagtgctgcatcttgctc-caactgccttgctccggaaatctgaagattttcttccaactaatacaatatttcgttgtcctcagGACCTGTTGGCTTTGGGAGAATCTATGGGCAATGTCAACACAGGCTTGGCCGATGAGAAAATTTCGAAGTGCGTGAAAGAAGTGGTCTGCTGCAGTTCCG
















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|29670363|gb|CB666638.1|CB666638
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88530273|gb|CI458653.1|CI458653
EST:     TTGACAATATGANTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: TTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29629980|gb|CB634989.1|CB634989
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|33682425|gb|CF310664.1|CF310664
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29622198|gb|CB627209.1|CB627209
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29669273|gb|CB665548.1|CB665548
EST:     AAGANNNNNNNAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATTTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|3760896|gb|C98150.1|C98150
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88830640|gb|CI078084.1|CI078084
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATCGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAAAGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29684935|gb|CB681210.1|CB681210
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|3760897|gb|C98151.1|C98151
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|7839221|gb|AU090632.1|AU090632
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGNCAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGNTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29623670|gb|CB628681.1|CB628681
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88993479|gb|CI110300.1|CI110300
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88527686|gb|CI455863.1|CI455863
EST:     CAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: CAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaccctggaaacttgaaaatctattttcttaactctatcatttgctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTGGACGAGAAAATCTCAGGTTGTGTGAGAGAAGTGATCTATTGCAGTTCTG
                           tcttaac  putative branch site (score: 2)
                aaaatctattttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaagagctggtttttgcttacatgcctcccaccctggaaacttgaaaatctattttcttaactctatcatttgctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTGGACGAGAAAATCTCAGGTTGTGTGAGAGAAGTGATCTATTGCAGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT