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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGGCGGCAGCCGCCTCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcggaattgtgcattcttaatcggccccttcgttttttttttgtgcctcag

Basic information

species Oryza sativa
transcript LOC_Os05g44360.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G060611_T01 (Zea mays), 5'ss of exon 1
GGCCGGCGGCAGCCGCCTCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcg-gaattgtgcattcttaatcggccccttcgtttttttt-ttgtgcctcag
 | ||||||| | || ||||||||||||| |||||||||||| ||||||||||| || ||||||||||||||| |||| |||||||||||||||||||| |||||||| | | |||||||                      ||  |||||||| | ||| || |||    ||| | |  ||||||||  |         || |   |||| |   | |||   | |||
CGGCGGCGGCGGGCGGCTCCGCAACGCCTTCGGGGGCGTGCTCTGCGCCTTCACGCTTCTCCTCATCGGCGTCGTCGCCTTCTCGATCCGCCTCTTCTCTgtaagatccgtttcgcccccg--------------------agcttccagatccagttcggcgctcgcaaagcgctccccgaattgtgtgtgt-------gctcacgcgttatgcctgttgctgcgcag

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G08410.1 (Glycine max), 5'ss of exon 1
GGCCGGCGGCAGCCGCCTCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcggaattgtgcattcttaatcggccccttcgttttttttttgtgcctcag
  |   |  || |  | || |  |||| | |||   ||| ||      |||||  || ||| | |||||||| ||||| ||||||||||| ||||||||||||||           |   |  || || ||| |       ||   || || ||          |||| ||| ||| ||   ||  |  |||| ||   |       | || | | ||  ||     
CACAACCACCACCTCCATCAGGCACGCGTTCGGCAACGTCCTCGCGTTCTTCATACTTCTCATGATCGGCGTTCTCGCCTTCTCGATCCGTCTCTTCTCCgtaag-----------catttttcctcattccgcag-atctggttacctgaacc----------tcgtttcg-gttccgacttttcgttttctcaacgcgattgcatgcttctatattcagcg----

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G01270.1 (Glycine max), 5'ss of exon 1
GGCCGGCGGCAGCCGCCTCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcggaattgtgcattcttaatcggccccttcgttttttttttgtgcctcag
  ||  |  || |  | || |  |||||| |||   ||| ||      ||||| ||| |||||||||||||| || || ||||||||||| ||||||||||||||           |   || || || ||| |       ||   || || ||          ||||  || ||| ||   ||  |  |||||||   |       | || |   ||  |||    
CACCACCACCAACTCCATCAGGCACGCCTTCGGCAACGTCCTCGCGTTCTTCATCCTTCTCCTCATCGGCGTTCTGGCCTTCTCGATCCGTCTCTTCTCCgtaag-----------catttctcctcattccgcag-atctggttacctgaacc----------tcgttccg-gttccgagttttcgttttcttaacacgattgcatgcttctaaattcagcc----

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 1
GGCCGGCGGCAGCCGCC-TCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatc--tgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcggaattgtgcattcttaatcggccccttcgttttttttttgtgcctcag
 |    || |  | ||  |  | || || | |||   |||  | |  | | | | |||| ||||||| || |||||||| ||||||||||| |||||||| || || ||  ||||    |  ||      | || |  ||  | |     ||  |   | | | | || |   ||    ||||| | ||  |      |     |                         
-GGGAACGCCGACTGCGATGAGGAATGCTTTCGGCAACGTTTTATCAGTCCTGATCCTCGTCCTCATTGGTGTCCTCGCTTTCTCGATCCGACTCTTCTCTgtgagttcactgatgtttctgcttggttgattc-atttca-gtgttcttcaattt--gttaggctttagatccga---tcggactagtttagatccgactaatctag----------------------

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|88395376|gb|CI611293.1|CI611293
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88388047|gb|CI590323.1|CI590323
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88391883|gb|CI603402.1|CI603402
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTATCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTAAACCTT
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAAC-TT
EST: gi|88689170|gb|CI732746.1|CI732746
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|29630981|gb|CB635990.1|CB635990
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88386226|gb|CI572843.1|CI572843
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88728375|gb|CI751885.1|CI751885
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88692423|gb|CI735998.1|CI735998
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88412871|gb|CI576135.1|CI576135
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|25797492|gb|CA753453.1|CA753453
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCCCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88693052|gb|CI736627.1|CI736627
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88422398|gb|CI689215.1|CI689215
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88431648|gb|CI576839.1|CI576839
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88420887|gb|CI620205.1|CI620205
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88406275|gb|CI596402.1|CI596402
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|29643810|gb|CB648817.1|CB648817
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88691581|gb|CI733659.1|CI733659
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88406160|gb|CI593940.1|CI593940
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTAATTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88305575|gb|CI631942.1|CI631942
EST:     CACCCTCCTCCTCATCGGCGTCCTCGCCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAANTTC
genomic: CACCCTCCTCCTCATCGGCGTCCTCG-CGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88390581|gb|CI609206.1|CI609206
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
EST: gi|88345883|gb|CI632356.1|CI632356
EST:     TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGNCTCTTCTCC                         GTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC
genomic: TCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctg ... tgtgcctcagGTGATTAAGTACGAGAGCGTGATCCACGAGTTCGACCCCTACTTCAACTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGGCGGCAGCCGCCTCCGCAACGCCTGCGGGGGCGTGCTGTGCGCCTTCACCCTCCTCCTCATCGGCGTCCTCGCGTTCTCGATCCGCCTCTTCTCCgtaagatctgatccgccccctccccccactccacctcgcgcggcggccagatccggctcgccgttcgtctcgcgtttcggaattgtgcattcttaatcggccccttcgttttttttttgtgcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC