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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgataagcttttctgttgtaacagtagggaagacaaattgtttaacaactgcattgcaacactgaacataaatttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g62070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62070.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G056283_T01 (Zea mays), 3'ss of exon 3
gtatgtttgata-agcttttctgttgtaacagtagggaagacaaattgt-------ttaacaa-------------------------ctgcattgcaacactga--acataaat---------------ttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA
||||| |  |||  |  ||||||||  |||| ||||||||  || || |       |||| ||                         || | ||  || | |||  |||  |||               |||||  |||| ||||||| |  || || ||||  ||||||||  | ||||||||  |||| || || || ||||| |||||||| |||||||| |||||||||||||| || |
gtatgctatatatggactttctgtttgaacattagggaaggtaacttatgtggatgttaataatcaaattttcttcactatattttttcttctttttaatagtgacgacaccaatagatatctggccactttattgacctgcagGAAGAACACGAAAAAGTTGTCAGGAGTGAATCATTAGCCATATGGCTGTCTAATATTGCAAATATGGTTCTCTTTGCTGCAAAAGTGTATGCTTCAGTAA

upper sequence: LOC_Os01g62070.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------gtatgtt--tgataagcttttct--gttgtaacagtagggaagacaaattgtttaacaactgcattgcaacactgaac--------ataaatttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA
                                         | |||||  |||| |  |||||     |||    ||    |   |   || |   | |     | |||| || | ||         |  | ||||||  |||| ||||||| || || |||||||| |||||||| || |||||||| ||| | || ||| | ||||| |||||||| |||||||| |||||||||||||| || |
gtatattatgtatgaacgacattagtgaaggtagcttatgtggatgttaatgatcaaattttcctcactgtgtttgtttctacttctttttttaagaaagtgagactgcatcaataaatgcttgataaccactttattgacctgcagGAAGAACGAGAAAAGGTTGCCAGGAGTGAAACATTAGCCATACGGTTGTCTAACTTTGCAAATATGGTTCTCTTTGCTGCAAAAGTGTATGCTTCAGTAA

upper sequence: LOC_Os01g62070.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099995_T01 (Zea mays), 3'ss of exon 1
gtatgtttgata-agcttttctgttgtaacagtagggaagacaaattgt-------ttaacaa-------------------------ctgcattgcaacactga--acataaat---------------ttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA
|||||||  |||  |  ||||||||  |||| ||||||||  || || |       |||| ||                         || | ||  || | |||  |||| |||               |||||  |||| ||||||| |  || || |||   ||||||||  | ||||||||  || | || || || ||||| |||||||| |||||||| |||||||||||||  || |
gtatgttatatatggactttctgtttgaacattagggaaggtaacttatgtggatgttaataatcaaattttcttcactatattttttcttctttttaatagtgacgacatcaatagatatctggccactttattgacctgcagGAAGAACACGAAAAAGTTATCAGGAGTGAACCATTAGCCATATGGTTGTCTAATATTGCAAATATGGTTCTCTTTGCTGCAAAAGTGTATGCTTTAGTAA

upper sequence: LOC_Os01g62070.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 2
-gtatgtttgataagcttttctgttgtaacagtagggaagacaa--attgtttaacaactgc--attgcaaca---ctgaacataaatttattt---gcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA
  ||   |  || ||  |     |||| ||| | |   | || |  ||   ||      ||   ||||  ||    |||||  |   | | |||   |    ||||||||||  || ||  | ||||  || ||||| || || ||  |  |||| ||||| ||||||||| ||||||||||||| ||||| ||||||||||| |
gttagcctaaatgaggctactacttgtcacatttgttgaaaccatgatgcatttgttcttgttgattgatacttttctgaatttctttgtgttttgtgtacatagGAAGAGCAGGATAATTTGGCTAAAAGCGAGACATTGGCGATTAGAATATCAAACATTGCAAACATGCTTCTTTTTGCTGCTAAAGTCTATGCTTCTGTCA

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|29661349|gb|CB657624.1|CB657624
EST:     ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAG                         GAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG
genomic: ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAGgtatgtttga ... ttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG
EST: gi|86829882|gb|CI288565.1|CI288565
EST:     ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAG                         GAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG
genomic: ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAGgtatgtttga ... ttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG
EST: gi|313084001|gb|HO213784.1|HO213784
EST:     ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAG                         GAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG
genomic: ATGAAATGGATACACTTACTGATCGTGGTTTTCTTCCAGGAATGTCCAAGgtatgtttga ... ttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattgtttaacaactgcattgcaacactgaacataaatttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA
       gtttaac  putative branch site (score: 3)
                                        tttattt  putative PPT
                              tgaacataaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgataagcttttctgttgtaacagtagggaagacaaattgtttaacaactgcattgcaacactgaacataaatttatttgcctgtagGAAGAGCGTGAGAAGGTTGCTAGGAGTGAGACTTTAGCCATCCGGCTATCGAACATAGCAAACATGGTTCTTTTTGCTGCGAAAGTGTATGCTTCTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC