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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctcctcggaacttactgaactgccctatgctgttactagtacttctgttcaaatattcatgtattacttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGAGCAAGCTGAAGAGGAGAAAGACGCAAAGGCAGCAGGAGCATCGGGATAG

Basic information

species Oryza sativa
transcript LOC_Os06g02620.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02620.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G153068_T01 (Zea mays), 3'ss of exon 14
gtaagctctcctcggaacttactgaactg------ccctatgctgttactagtacttctg-----ttcaaat---attcatgtattacttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGAGCAAGCTGAAGAGGAGAAAGACGCAAAGGCAGCAG---GAGCATCGGGATAG
||||||   ||| |   | |    || ||       | |||||| |   | || | ||       | ||| |   | |||  ||| |  |     ||| ||||||||  | |||||||| | ||||||||||||||| |||||||| |||||||  ||||| ||||| ||||| ||||||||||   ||||||||||    
gtaagcaagcctagccgcctctcaaaatggagtagtcttatgctatctatcgtgcatccaactgctgcaagtgagactcacatatgatgt-cctgcagAAATTTGACGTCTAGACAGCGGGAGCTGATCGAGGAATTCGCGAAGGAGGAGCAAGGCGAAGACGAGAAGGACGCCAAGGCAGCAGCTGGAGCATCGGGG---
















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|396941303|gb|HO188512.1|HO188512
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|86525359|gb|CI165565.1|CI165565
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|218486942|gb|FG960669.1|FG960669
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|38477689|gb|CF961822.1|CF961822
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGG
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGG
EST: gi|88243653|gb|CI244050.1|CI244050
EST:     CCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: CCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|88832398|gb|CI019339.1|CI019339
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|109712340|gb|CI104948.1|CI104948
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|88269750|gb|CI381048.1|CI381048
EST:     CATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: CATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|88224010|gb|CI223859.1|CI223859
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|29614537|gb|CB619550.1|CB619550
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGG                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|87018983|gb|CI256868.1|CI256868
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|88274169|gb|CI394575.1|CI394575
EST:     CAGTATTTCCACTTCAATGTCAACATCCCTTC                         GAATTTGACACCGAGACAGCGCGTGCCTGATCGAGGAATTTGCGAAGGAAG
genomic: CAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTG-CTGATCGAGGAATTTGCGAAGGAAG
EST: gi|86846261|gb|CI339852.1|CI339852
EST:     CAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: CAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|22304698|gb|BQ905920.1|BQ905920
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACA--GCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|88907776|gb|CI091174.1|CI091174
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
EST: gi|86488478|gb|CI131111.1|CI131111
EST:     TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGC                         GAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA
genomic: TCATCGTACTATGGAGATCAGTATGTCCACTTCAATGTCAACATCCCTGCgtaagctctc ... ttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctatgctgttactagtacttctgttcaaatattcatgtattacttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGAGCAAGCTGAAGAGGAGAAAGACGCAAAGGCAGCAGGAGCATCGGGATAG
                            aaatattcatgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctctcctcggaacttactgaactgccctatgctgttactagtacttctgttcaaatattcatgtattacttatacacagGAATTTGACACCGAGACAGCGCGTGCTGATCGAGGAATTTGCGAAGGAAGAGCAAGCTGAAGAGGAGAAAGACGCAAAGGCAGCAGGAGCATCGGGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA