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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaccaaggaggcagtaacaatttaagaatttgcatgatagttataatgctagtaaattttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG

Basic information

species Oryza sativa
transcript LOC_Os07g23200.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g23200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G174246_T01 (Zea mays), 3'ss of exon 9
gtacaccaaggaggcagtaacaatttaagaatttgca-tgatagttataatgctagtaaattttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG
             |  |    || | || |||||| | |||| |||    | | ||| |   |||    | ||  | ||||| |      ||||||   | |     |  || | | | ||||| |||||  | |||||||| ||||| |||||||||||||| ||||| |||||| | |   || | ||||| ||||||||  |||||||| | ||  | |
-------------gtgg-gttaagtgaataatttggaatgatggttcctttaccagttacagttgc-aatgctggttcctatac------cagttgcactgaagctctcaatttctacgcagGACCTTCGGCGAAAACTTCCAGTTACCCGTACTCTTTTCCCCTGGCATAACACACTGGTGTTCGGTCTTACGAGAGACCTTGCCAAAGAATTAGCGCTTG

upper sequence: LOC_Os07g23200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G010136_T03 (Zea mays), 3'ss of exon 9
gtacaccaaggaggcagtaacaatttaagaatttgcatgatagttataatgcta-gtaaattttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG
|||    |||     |||       | | |  |   ||   ||||| | ||||| || |   | ||    | |  | | |    || | |    ||    |     | || |  |||| ||||||||||| || |||||||| || || |||||||||||||||||||| |||||| | ||  |||| ||||| ||||||||  ||||| || | ||  | |
gtaggataagtgaatagtt-tggaatgatagctcctataccagttacagtgctatgtcatcctcgtcatcattgctcctttgtgtcagttgcactgaaactctccatgattt--gtgcgcagGATCTTCGGAGAAAACTTCCAGTGACCCGTACTCTTTTCCCATGGCATAACACACTGGCAGTCAGTCTTACGAGAGACCTTGCCAAACAATTAGCGCTTG

upper sequence: LOC_Os07g23200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
gtacaccaaggaggcagtaacaatttaagaatttgcatgatagttataatgctagtaa--attttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG
                       ||| |  ||||     ||   |  | | | |  |   |  ||| |  |   ||   |   | | || |   || | ||| ||||     | | |   ||||||||||| ||||| ||||| ||||| || || || |||||||||||||||||  |     | |||||  |||||||| || | |||||||| |  || |
-----------------------ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG

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|58685723|gb|CK074410.1|CK074410
EST:     GAATCATACATGAATTTGTCTGATGCAACCTTCAAG                         GATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCAT
genomic: GAATCATACATGAATTTGTCTGATGCAACCTTCAAGgtacaccaag ... atgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCAT
EST: gi|86528479|gb|CI168685.1|CI168685
EST:     GAATCATACATGAATTTGTCTGATGCAACCTTCAAG                         GATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC
genomic: GAATCATACATGAATTTGTCTGATGCAACCTTCAAGgtacaccaag ... atgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC
EST: gi|86494262|gb|CI136895.1|CI136895
EST:     GAATCATACATGAATTTGTCTGATGCAACCTTCAAG                         GATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC
genomic: GAATCATACATGAATTTGTCTGATGCAACCTTCAAGgtacaccaag ... atgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC
EST: gi|27547453|gb|CA765564.2|CA765564
EST:     GAATCATACATGAATTTGTCTGATGCAACCTTCAAG                         GATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC
genomic: GAATCATACATGAATTTGTCTGATGCAACCTTCAAGgtacaccaag ... atgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG
                                       ttatatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaccaaggaggcagtaacaatttaagaatttgcatgatagttataatgctagtaaattttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC