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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT

Basic information

species Oryza sativa
transcript LOC_Os07g08880.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 2
atgctttgctggcctatgctatctattaaattgatttatgtat-tgcattaatatcatcattttatttgattttctcatccctttactaaca-atatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
||   | |    | | |  ||  | |  |  |  ||  |  || || || |  ||  | | ||  |||  |  ||| ||| |||   ||| | || || |||||| |||||||| ||||||||||||||||| |||||||||||||||||||                   
atagatgg--aactttttttacttgtatatgtatttcttaaatctgaatcatcatttttacttgttttattcctctaatctcttctgtaaaacatgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG

upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
--atgctt-tgctggcctatgc-tatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
  ||   | |       |||   ||| ||| |  ||    | ||| |     |  |     |   ||| |  |  |   ||||   |      |  | || ||| |  |||||||| |||||||| ||||||||||||||| | ||| | ||||                   
atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactcc---gctgtttg-cagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------atgctttgc-tggcctatgctatctattaaattgatttatgtattgcatta---atatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
                                                                              ||| |  || | |  | | || |    |  | ||| | | |  | |  ||    |  | |  | ||| |    ||   | ||  |||         | |  |||||  ||||||||||||||||||||||| |||||  || | ||| |  |||                   
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 3'ss of exon 2
-atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttat-ttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
     || |||      |   ||||     |  |||   |  | |  |  |  ||| |  |    | ||  |  ||    || |  |||     |||| ||| |  ||||||||||| ||||||||||||||||| ||| | ||| | ||||                   
cgattttggctttgtagttacatcttcctgaaagatgccttaaatagaaaacaatccttgtgccgtattagtaatcgtgaccttcaactggtg-tatg-cagTTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------------atgctttgctggcctatgctatctattaaattgatttatg-tattgcattaatatcatcattttatttgattttctcatccctttactaa---caatatgac----agGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
                                                                       | |||  || |     | | | |  | |    | || |  | ||    |  | |    | ||   ||  || |||  |    |||| ||   |  ||| ||    ||||  |||||||||||||||||||||||||| || ||  | ||| | || |                   
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgtgttcttatcaagcttctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

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|58603106|gb|CK013634.1|CK013634
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATG
EST: gi|33822155|gb|CF336893.1|CF336893
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATC
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATC
EST: gi|58679044|gb|CK067731.1|CK067731
EST:     TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGT                         GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT
genomic: TTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaattt ... aatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT
                                      tactaac  putative branch site (score: 0)
     atatcatcattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG