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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatctagctagggcatcgcgtca...

Basic information

species Oryza sativa
transcript LOC_Os07g16970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctc-tctctctctcccgcccggatcgatctagctagggcatcgcgtca
|||| ||| ||||||||| ||||||||||||||||||||||| || || ||||||||||||||||||||||||||||||||||| || || |||||||||||    | |    | |   | | |||  ||  || |   ||||||||| |||  || ||   | || |      |||||  |      ||  |||   |  
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgc-ctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccg--gatcgatctagctagggcatcgcgtca
             ||||| | || || ||| ||||||||| | || ||||| |||||||||||||| |||||||| || ||||| |||||| ||||||||||  ||  |   | | | | ||| |   | ||| | ||  |   ||    |||| |    |   |||     |  | |||||  ||                
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttct-tttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag----------------

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 5'ss of exon 2
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctct---ctctctcccgcccggatcgatctagctagggcatcgcgtca
                 ||| |||||| |||||||||||||| || ||||| || |||||||||||| |||| ||||| || || || ||       ||||||     | |   |||         |    |   |   |   || |   || | | ||   | ||| ||  | |     | |  ||                
----------------AACGAGGAGTATGACGTGATCGTGCTGGGCACGGGTCTGAAGGAGTGCATCATCAGTGGCCTGCTGTCGGTGGACAAGAAGAAGgtgcgggacctagacatgcgcgcgaatgctgcaaccgggcctgcttttcttcgcgcgctggccgctcaccatcgcaacctgttgcag----------------

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggt--ctccttctccatct---ctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatctagctagggcatcgcgtca
|||      || |||||| |  ||||| |||||||| || ||||| || || |||||||| || |||||||| || || ||||| |||||||| |||||||||||  ||| | ||| ||||   |  | | |   | |     ||  | | | | | | | | | |   |           |  |||        | |   ||  
CCGAGATTTCGTCATGGATGAAGAGTATGACGTGATTGTACTCGGCACTGGCCTCAAGGAATGTATCCTCAGTGGACTTCTCTCTGTCGATCGTCTCAAGgtggtgcctcttcctcgatctgaaccttttataggtttgcagatcagtgtttttgtttgtttgttttgtttttattt---cctttctcttcttctccttaggt--

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatc--tagctagggcatcgcgtca
| || |   ||| ||||| |  || || |||||||| |||||||| || || |||||||| ||||| ||||| || || |||||||| ||||||||||||||||  ||   ||||  |||  |||   |     | | | | | |  ||       |       || ||  | | | ||    | |  | |  |  | |   
CGGCACCTTCGCTATGGATGAAGATTATGACGTGATTGTGCTCGGCACTGGCCTCAAGGAATGCATTCTCAGTGGACTGCTCTCCGTTGATCGCCTCAAGgtggcgtctccctcc--ctcgatctgggttgacatgtgtgtgtgtagcttggagattgatagcttcgcgttcaggttgaatgtttgagatgcaagtgtgctg

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S167_1V6.1 (Physcomitrella patens), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctcc-atctctctctctctctctctctctctctctctctctctctctctctctctcccgcc-cggatcgatctagctagggcatcgcgtca
  |  |   | ||||||| |  |||||||| ||||| ||||| || || ||||| ||||||||||||||||| || || |||||||| ||||| ||||||||||      || |  |||    |   ||| | |  |||   |  | |  |       |   |||||  |     |   |   | |   || |  || |  |
TGGAGCCGGCACCATGGATGAAGAGTACGATGTGATTGTGCTGGGCACCGGGCTGAAGGAGTGCATCCTCAGTGGGCTACTCTCCGTGGATCGTCTCAAGgtgggtgggatcgcagatcgtggttgatctgtgtgactcgggcggtgtggcgtagctgccggctctctgggtgtagcgtggatttgt--ggtcggcgaggga

upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatctagctagggcatcgcgtca
      |  ||||||||| | |||||||||||| || ||||| |||||||| ||||||||||||||||||||||| || || || || ||||| ||||||||||  |  ||||| |||    |         |||||||| |                                                          
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtggg-tttttctcgatcggagttggaagacatctctctcgcag--------------------------------------------------------

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|29624786|gb|CB629797.1|CB629797
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88735266|gb|CI758774.1|CI758774
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88408099|gb|CI601577.1|CI601577
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88735048|gb|CI758556.1|CI758556
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|29616692|gb|CB621704.1|CB621704
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88407824|gb|CI588853.1|CI588853
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88744533|gb|CI767893.1|CI767893
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|58692091|gb|CK080778.1|CK080778
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
EST: gi|88407852|gb|CI588881.1|CI588881
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAG                         GTGCTGGATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctcct ... ttgtcaccagGTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatctagctagggcatcgcgtca

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC