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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgccaggaattgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 28
tttgtgccaggaat-tgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaa---ccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
  ||   ||   || ||  | |   | ||  |||    | | |  | ||| |      | |   || |  ||| || ||||     |  | | |   |||||||||| || ||||| |||||| ||||||||||||||||||| || |||
--tgcatcaaatatatgtcagtgtttatctctgtatgttgctattaaagtgtcaaaagtatttgtgtt--agcagtgctaaatgtttcctcatcaccttttcagGGAGCCATTGATTACAAATATCATGTGGAGAAACTTAATTATCATG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 28
---tttgtgccaggaat-tgctaatacctttcaatgtgcaattcaaa---cagagttttttgtttctgcatgctgaagctgtcctaaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
     ||   ||    | ||  | ||  | ||  |||    || ||    || |  | ||| | |  |||     ||   ||       || | | | | |||||||||| || ||| |||||||| |||||||||||||||| || || |||
ttagctgcagcaaatttatgtcagtatttatctctgttgctttgaagtgtcaaaaatatttatgttagcagcgctaaatggt-------ttctcatcatcttttcagGGAGCCATTGGTAACAAATATCATGTGGAGAAACTTGATTATCATG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 29
tttgtgccaggaattgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaaccttgt-taccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
                    |   |||   | |  | ||||||   |             |||  ||   ||| | ||||| |  | |   | | ||||||||||||  | |||||||||||||||||||| |||||   | ||  |
-------------------gtttgtttggctttttatttcaaattaaaa-----------gcagacttgggct-tactaacatcttatgtttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 29
-----------------------------------------------------------tttgtgccaggaattgctaatacctttcaatgt----gcaattcaaa---cagagttttttgtttctgcatgctgaagctgtcc----taaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
                                                           ||| |    | |||| |||| |   | |||       |  |||||||   || |   |    |     ||  ||   |||  |     ||    |  |   | | ||||||||||||| | |||||||||||||||||||| ||||| ||| ||  |
gtttggtttggtttggtttgattggatctcttactatactatgagaatttatacgcattttttttattgcaatttctaaaattatacaaaaacaaggttattcaaaatccaaatactcacttgaagacagacttgggcttactacgatatatcttatgtttggctttcagGGAACCCCTTATAACAAATGTCATGTGGAGGAACTTGATCGTACAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 30
----tttgtgccaggaattgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
     |||  |  |   || | | | | |   || | |  |     |       |||  ||| || | ||  | ||  |  | |  |  |||     || |||||||||| |||||||||||| |||||||||| || ||  | ||   |
gcaaattgaac--gctcttacaagtgcatgcaaaggaggtacatccattttccctttgatttttgtaggc-aatgcattgatgatatc-ttattcatttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG

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|88351169|gb|CI623391.1|CI623391
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGGAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     CAGAACCACCTACTGACCATCTTATGCCAGAGACCACCAGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: CAGAACCACCTACTGACCATCTTATGC-AGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCAACAGTTGGCAGAAG                         GGAACCCTTGAATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGA-TAACAAATGTCATGTGGAGAAACTTAATCATAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttttgtttctgcatgctgaagctgtcctaaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
                             tcctaac  putative branch site (score: 1)
                                           ccttgttttc  putative PPT
     ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgccaggaattgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaaccttgttaccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA