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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagtattttcatgctgtttaaaagaacatgtgtttcaaatagttataaacataaattttcactgttcccattatattatctaacatagtcatttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA

Basic information

species Oryza sativa
transcript LOC_Os07g31460.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G474236_T01 (Zea mays), 3'ss of exon 6
tcagtattttcatgctgtttaaaagaacatgtgtttcaaatagttataaacataaattttcactgtt-----cccattatattatctaacatagtcatttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA
    | |||   |||  | |   | || |||   |  |||  |||  ||  | |  | || | | ||      |   | |||   |||||| ||   || | ||||||||||| | ||||| |  ||||  |||||| ||| |||||||||||| |||||||||||||||||||||||||||| |||||||||||||||||||||
----tttttgtgtgcgatgttgta-aagatgctgtctaaagtgtttcaagtacacgtgttgaattttattgatctgctgtatcggctaacaaaggagttatgcagGATGTTGGCTGATTTATACAATGCAAGATGGCAAAAGTTGCGAGTTGGAGTCATATGATTTGATGTCAGCTAATGATGCTCCAGAGAGGGATCCAATGGA

upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA03G40660.1 (Glycine max), 3'ss of exon 14
tcagtattttcatgctgtttaaaagaacatgtgtttcaaatagttataaacataaattttcact-gttcccattata----ttatctaacatagtc-atttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA
     | || |||    |||  | |  ||     ||| || || |  | |||    |  || || | | |   ||||    || | | | |||    | ||   ||| |||||| |  | || |  |   ||| |  | | |  |  ||| | |   ||||||| ||||||||||| |||||||  ||||| ||||||||||||||
-----aattccatttgatttctatgtccaccccattctaa-aggtgcagacactgctgctctcttgatgctgatataaaaattttgttatatatctgacttcgtagGTTGTTGGGTCGTGTATAGAACATTTGGTAACGAGATGTTTGAGCTTGTAGCATATGAGTTGATGTCAGCCAATGATGCACCAGAAAGGGATCCAATGGA

upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 14
tcagtattttcatgctgtttaaaagaacatgtgtttcaaatagttataaacataaattt-tcactgttcccattatat-tatctaacatagtcattttt-cagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA
    || || |||    |||  | |  ||     ||| || || |  | |||    | | |   || |   || | |  | | | | |||      |    ||| |||||| |  | || |  |   |||||  | | |  |  ||| | |   ||||||| ||||||||||| |||||||  ||||| ||||||||||||||
--tataattccatttgatttctatgtccaccccattctaa-aggtgcagacactgctctcttgatgctgatataagaaatttgttatatatctggctgcgtagGTTGTTGGGTCGTGTATAGAACATTTGATAACAAGATGTTTGAGCTTGCAGCATATGAGTTGATGTCAGCCAATGATGCACCAGAAAGGGATCCAATGGA

upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv14s0030g01930.t01 (Vitis vinifera), 3'ss of exon 14
tcagtattttcatgct-gtttaaaagaacatgtgtttcaaatagttataaacataaattttcactgttcccattatattatctaacat---agtc--atttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA---
      |||  |||   ||||         | |  | |  | ||    ||   | || |  |  |  |   ||||| |  | ||| |    | |    | ||  ||| |||||||| || |||||  |     ||    | |     ||  | |   ||||||| ||||||||||||||||||| ||||||||| |||||||||||   
------tttatatgagagtttttctctctttatcatccgcacagcctcaagttttaactcacgtttattatattatgtgttttaataattgaatttggtcttgtagGTTGTTGGATTATATACAAAGTAAACAATA---AGATGCAAGAACTTGTGGCATATGAGTTGATGTCAGCTAATGATGCTCCAGAGAGAGATCCAATGGATTG

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|29676465|gb|CB672740.1|CB672740
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAAGATGCTTGATG
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATG
EST: gi|29616585|gb|CB621597.1|CB621597
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAGGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
EST: gi|29624539|gb|CB629550.1|CB629550
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAGGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
EST: gi|29676466|gb|CB672741.1|CB672741
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
EST: gi|27548254|gb|CA766230.2|CA766230
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAGGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
EST: gi|29621977|gb|CB626988.1|CB626988
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAGGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
EST: gi|29681352|gb|CB677627.1|CB677627
EST:     ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG                         GATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT
genomic: ATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAGgtgatccggt ... catttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaacataaattttcactgttcccattatattatctaacatagtcatttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA
                                 atctaac  putative branch site (score: 2)
                                            tcatttttc  putative PPT
                         attatattatctaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagtattttcatgctgtttaaaagaacatgtgtttcaaatagttataaacataaattttcactgttcccattatattatctaacatagtcatttttcagGATGTTGGATAATTTACAAGATGCTTGATGGCCAAACTTGCGAGTTGGATTCATATGATTTGATGTCAGCTAATGATGTTCCAGAGAGGGATCCAATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG