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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt...

Basic information

species Oryza sativa
transcript LOC_Os07g46450.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G340359_T01 (Zea mays), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagta-acagtttcaatcaactt----
|||||| | ||||||||| |||| |||||||| ||||||||||||||||||||||||||||||||| |||||||||| ||  ||||||||| ||||||  || | |||||     || | |  ||  |||| ||||||||||     || ||   |||| ||| ||   ||   |   |  | ||    
GCTAGAAGTAATGCAATCCTACAGGCAAGTTTAGAAAGAAGAAAACAAGCACTACATGAGCGCCGTGTGGCTCTGGAACAAAATgtatgct-tattctactagcttatgat----ttgtctgcttttatgcatccaaaatatatcagaagttcagccatttgttgtgtgcatacttgttatattttgtt

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G036872_T02 (Zea mays), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacag---tttcaatcaactt--
|||||||| ||||||||| |||| |||||||||||||||||||||||||||||||| ||||| ||| |||||||||| ||||||||||||  ||||||  || | ||  |     || | |  ||  |||| ||||||      |     | |    || ||| || | ||    |  |    | ||  
GCTAGAGGCAATGCAATCCTACAGGCAAGTTTGGAAAGAAGAAAACAAGCACTACACGAGCGTCGTGTGGCTCTGGAACAGGATgtatgccttattctactagcatacaa-----ttttctgcttttatgcatccaaaccccatttgttttgtgcatatttgttgtgaaagggcctctagctgagttgg

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatg-----ctatattcttttaccc-tatgaattagtt--atttcattccatgcttccaa-----aatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt------------------------------------
|| | |||||||||||| |||||||| ||||||||||||||||| ||||| |||||||| || ||  |||| || || || ||||||||     | ||     || |     ||||   |  |  | ||||||  ||    | |      | | |  |  || | ||| |   | ||       | | | |   |                                      
GCAAAAGGAAATGCAATTTTACAAGCTAGTTTGGAAAGAAGAAAGCAAGCTCTACATGACCGTCGGCTGGCCCTTGAACAAGATgtatgtgtatccatcccggttcatttgcatgagggaaatgcacttcattggatatcccaagcggttattttagtataagtgtcatcgcat-tatccctcctctgagtaggccatatgcctgtcatttggggatgtttctgtacgttcag

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgc-tatat-tcttttaccctatgaattag-----ttatttcattccatgcttccaaaatatgctgaaa-----atttcaccatctgtagtaacagtttcaatcaactt----------------------------------------------
|| | ||| |||||||| |||||||| || |||||||||||||| |||||  ||||||| || ||| |||| || || || |||||| || |||   || |  ||||| |||   ||     | ||||  ||      || ||| |  |||   |      |||  |      || |  ||  | ||  |   |||                                              
GCGAAAGGGAATGCAATTTTACAAGCTAGCTTGGAAAGAAGAAAGCAAGCTTTACATGACCGTCGTCTGGCCCTTGAACAAGATgtaagcgtatccatcctagaccctttgaccaaggaaaatgattttctttgtgtatttcaagacttgcaagattagttattgtaatgcaggttgccacgttgtccttgcccttattcaggtttttacaattattttattttattttattttttgttcag

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ24423 (Selaginella moellendorffii), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt
|||| ||||||||||||  | ||||| |||||||||||| |||| |||||||| ||||| |||||  | ||||| || || || |||||||   | || ||  ||| |   ||  ||||   |||   ||  | ||||      || |||   ||                             
GCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCATGATCGCCGGCTCGCTCTTGAACAAGACgtatgct-cgtgctattttcctttcc-ttttttatgagattt--tgacttcaaa-----ttgtaaacaccag----------------------------

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ23838 (Selaginella moellendorffii), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt
|||| ||||||||||||  | ||||| |||||||||||| |||| |||||||| || || |||||  | ||||| || ||||| |||||||   | || ||  ||| |   ||  ||||   |||   ||  | ||||      || |||   ||                             
GCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCACGATCGCCGGCTCGCTCTTGAACAGGACgtatgct-cgtgctattttcctttcc-ttttttatgagattt--tgacttcaaa-----ttgtaaacaccag----------------------------

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|25800836|gb|CA756797.1|CA756797
EST:     AACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT                         GTTTCAAGGTTGCAAGAGCAGCTACAAGCTGAAAGAGATCTTAGAGCTGCA
genomic: AACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctata ... gtacctctagGTTTCAAGGTTGCAAGAGCAGCTACAAGCTGAAAGAGATCTTAGAGCTGCA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt

- - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG