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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatagtgtaaaaattgctagtgatgttatgttatcatttagatagtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA

Basic information

species Oryza sativa
transcript LOC_Os07g46450.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46450.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G340359_T01 (Zea mays), 3'ss of exon 11
-----taatagtgtaaaaattgctagtgatgttatgttatcatttagatagtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA
     || |  | |  |     | | |    |     |  || || | ||  | ||  | | |  || |  || | || ||  |  |||| ||||  ||  |||||||||||| ||||||||| || ||||||||||||||||| |||||| |||||||| |||||||||||||||| |||||||| || |||||||||||||| 
agttgtagttttatgcagtcatcaaattcgctagaaattgcactttgttatatcat--atatccagctattttttaaataaa-tcataaatccatgctt--gcagAATTTTGAAAATGATGCATACCGTTGCTTCTCATACTGCCGAGAATAGAATGACTCCATCAGCAGTTGCTGCATGTATGGCCCCACTCTTGTTGCGTCCC

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G036872_T02 (Zea mays), 3'ss of exon 11
-taatagtgtaaa--aattgctagtgatgttatgttat-catttagatagtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA
 |  |||| | |   | |    |    || || |   | || || |  |  | ||  | | | | |    || ||||| |  |   ||| | ||  ||  ||||| |||||| ||||||||| ||  |||||||||||||||| |||||| |||||||| |||||||||||||||| |||||||| || |||||||||||||| 
cttgtagttttatgcagtcatcaaatttgctaggaattgcactttgtgatatcat--atatcagactgtttttttaactaaatcacaaatcaatgctt--gcagACTTTTGAAAATGATGCATACCATTGCTTCTCATACTGCCGAGAATAGAATGACTCCATCAGCAGTTGCTGCATGTATGGCCCCGCTCTTGTTGCGTCCC

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 11
-----taatagtgtaaaaattgctagtgatgttatgttatcatttagatagtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA
     |  || |||     ||  ||     |   |||  |  ||  | |   || |  |   |||   |  |  ||   | ||    | ||      |||  |||||||||||| |||||||   | ||  |  | || || |   | ||||||||||| |||||||| || || || ||||||||||| || ||||||||||| 
tttcattttactgtttgttttaataaattggacgtgtgttgcttgtgtttacttctttatccctgatgagctgttttttacgc---aagaatttgccttt--cagAATTTTGAGGATGATGCGAGCAGTATCAGCACACACAGACAACAATCGAATGACGGCATCAGCTGTCGCCGCGTGTATGGCTCCACTTTTGTTGCGTCCC

upper sequence: LOC_Os07g46450.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 3'ss of exon 11
taatagtgtaaaaattgctagtgatgttatgttatcatttagatagtttatcaacaactggccaa--attcttaac--aagcttgtaaaaccattttttgg---cagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA
      ||| | |  | |  |   ||||   ||  | ||  |   |  | |  ||| |||   |    || || ||  |||  |||  |    |||||||    ||||||||| ||||||||||   | ||  |  | || || |  || ||||||||||| ||||| ||||| ||||||||||||||||| || ||||||||||| 
------tgttacagctacctgct-tgtttgcttcacgttgtgtatgcctctttacagctgaagagctgtttttcactcaagagtgttgagtatttttttgctttcagAATTTTAAGAATGATGCTAGCAGTATCAGCACACACAGACGACAATCGAATGACCGCATCTGCAGTCGCTGCCTGTATGGCTCCGCTTTTGTTGCGTCCC

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|58670024|gb|CK058710.1|CK058710
EST:     GGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAG                         AATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
genomic: GGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAGgtcagtgtac ... tttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
EST: gi|44679468|gb|CR292902.1|CR292902
EST:     GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAG                         AATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
genomic: GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAGgtcagtgtac ... tttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
EST: gi|58671855|gb|CK060541.1|CK060541
EST:     GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAG                         AATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
genomic: GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAGgtcagtgtac ... tttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
EST: gi|88422394|gb|CI689211.1|CI689211
EST:     GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAG                         AATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT
genomic: GCGGCAATATCTGAGACATTTCCTGAGCCTAATAGGCGGCTGCTACAGAGgtcagtgtac ... tttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA
                      tcttaac  putative branch site (score: 2)
                                         ccatttttt  putative PPT
                                    taaaaccatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatagtgtaaaaattgctagtgatgttatgttatcatttagatagtttatcaacaactggccaaattcttaacaagcttgtaaaaccattttttggcagAATTTTGAGAATGATGCACACTGTTGCTTCTCATACTGCTGAGAATCGAATGACTGCATCAGCAGTTGCTGCCTGTATGGCTCCTCTCTTGTTGCGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat