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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 3
----tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacg-attttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
    | ||       |        |||   | |||   |  | |   |    |     | | |  |||     | | |||  |||||||| |||     |||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||
aaacttctttaacacacacacacacatatgacatatgtatgtatgtgtacacacacattatttccttttgatgatgcattaaaattttgtctct-----tgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaatt--ttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
|    ||  || | |   |    |||| ||      ||||  |   | |    |  |  |  ||    |  ||  |   ||  |      |  |  ||  ||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||||
tctccataatttgttg--taagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 3
---tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgat-tttaattttgtttctcttt-ttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
   || |     ||  |  |            | |    |||||||     ||      |  |  |||   | |||  | ||||     |  | | | ||| |||||||| ||||| |||||  ||||||| ||||||||||||||||| |||||||||
aaatgttttcaattgaggtgtcttgctgttgtttcgattttttcct-----agaaataataatcattcgattgcgacatctaataggaataatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcagg--tacgattttaatt--ttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
    ||   |    ||      ||   ||  || |   || ||  ||   |   ||  | ||  || |  |  ||  |  |||  |      |  |  ||  ||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||||
----gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
---tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
   || |    |||     |   | ||   |     |  ||||    |  ||       || |      |  || |  | |     ||   |  | ||| |||||||| ||||| |||||  ||||||| ||||||||||||||||| |||||||||
aaatgttttcagttgaa--gtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaac-acctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctc-tcttatttcaggtacgatt--ttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
  |  ||  | |    |  |  |   |  || |  ||||     || |||     | | || | |    |   | |  ||  | ||||   ||| ||||  ||||||||||||||||||| || ||||| || |||||||||||||| |||||||||
--caaattttcatcatgaagagttggaactaaaagctttgttacttaaagatatgcattttgtgtttattcttagtagtttttgttgtgagtctctttg-cagGGTGGATTTGATATGATATGTAGTGGAAGAGACAAGATTGAAACTCCAGAGCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------tgctgatggttaggt----cgctgcatgaaatataca-cacttttcctt--tttaaggggctctcttatttcag---gtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
                   | |  | | || |      | || ||  | || |  | || |  |||||  || ||    ||    | ||| ||    |  | || ||||| | ||| |  | |  | ||||||| ||||| |||||||||||||| || ||||||||||||||||| || |||
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 3
-tgctgatggttaggtcg-ctgcatgaa-atatacacacttttcctttttaaggggctctcttatttcaggtacgattttaatt--ttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
    | | |   |  |   ||   ||   || ||  |||     |     | | |   |    | |  ||   | | ||  |||  |||| |   ||| |   ||||||| |||||||||||||||||||| || |||||||||||||| ||||| |||
gcattcacgcacattttatctatgtgctcatgtatgcacacaggc-----atgtgataccaccaatatagcctcaacttgtattctttgtcttgttttatatcagGGTGGTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0059g01220.t01 (Vitis vinifera), 3'ss of exon 3
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaattttgtttc-tctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
   |||    |   |   | ||      || |     | |  || | | | || ||| || |      | | || ||| || ||||   |  |||||| ||||||| ||| ||||||| || ||||| ||||||||||||||||| ||||| |||
gtttgagtaatgtattttttcagacttcattctgtagtgtgtttatcaggtggttctttt-tggggattcccatcttacttatgttgaattcttttgacagGGTGGCTTTCATATGATATGTAGTGGCAGGGACAAGATTGAAACTCCAGAACAG

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|58598594|gb|CK009122.1|CK009122
EST:     GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAG                         GGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG
genomic: GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAGgtatagcaac ... tttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG
EST: gi|218497540|gb|FG953486.1|FG953486
EST:     GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAG                         AGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG
genomic: GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAGgtatagcaac ... tttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG
EST: gi|58675628|gb|CK064315.1|CK064315
EST:     GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAG                         GGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG
genomic: GCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAGgtatagcaac ... tttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaggggctctcttatttcaggtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
                            ttttaat  putative branch site (score: 3)
                            ttttaattttgtttct  CT-rich tract
                           attttaattttgtttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG