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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g01890.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 4
gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgcctttt---atcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
|||||| ||| ||||||     ||   | || ||| ||||||  |   |||||  ||  || |   | |||     | |||| |||   ||||||||  || |||||| | ||||| ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
gtaagtgaatcgttctggccatctggagaaggatttttgttgcgtaaccttgccatt--gagactgtcctaatcatagtgccatttcaaatcttgtttcagACTCCTTGCGATTGCGGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgcta-tcttaactgcctttta--tcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
|||||| |||  |||||     ||   | || ||| ||||||  |   |||||  |||| | |  || ||| || |||   | ||  |  |||||||  || |||||| | ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
gtaagtaaatagttctgagtgac-tcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatc-ttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
         ||  ||||||   | | | || || ||  |  |        ||  |  |    | | |  | |  ||   |  || ||    |  ||  || ||||| |||||||||||||| || |||||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
--------gtaaatctgagcttcatgaagtggagttgcttct--------tttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 3
gtaagtaaatagttctgagtgac-tcaggtagaatta-ttgttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
         || ||||||    | | | ||  | ||  || ||   |||   ||   ||| |   |||   |   ||  |||   |    ||||    || ||||| |||||||||||||| || |||||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
--------gtaattctgaacttcatgaagtgaagttgcttcttttgtgg---tgaagttttgc--tcaaattggtttttctgttgtgatccttgc---agACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaaatagttctgagtgactcaggtagaattattg---ttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
                       | | ||   ||| |||   ||| |   || |  |  |    | |  |  |  | ||| ||| |  | | | ||  |||  | || ||||| ||||||||||| ||| |||||||||| || |||||||| || || ||| |||||||||| ||||||||||||||||||
----------------------gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgcttggt-tttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g04320.t01 (Vitis vinifera), 3'ss of exon 3
-----gtaagtaaatagttctgagtgactcaggtagaatt--attgttgg-atggacttgctctttcgatatca--tgctatcttaactgccttttatctt----gttcta--gGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
     || |   |  ||   | | ||||    |||||| |  | | |||   | |  ||||| |     | |||  |||         |||  || ||| |    ||||||  ||||||| ||||| || |||||| || ||   |||||||| ||||||||||  || || ||| |||||||||||||||| ||||||||||||
gtaatgttaaccatcagcaat-attgacctctgtagaactccacttttgatgtaggtttgctatcattttttcaattgcagctgctgatgcacttaatcctttatgttctacagGCTCCTCTCAATAGCTGAGGAGGCCATGGGGGAGTTCCTTTCAAAGGCTAAGGGAACTGCTGTTGATTGGGTCCAGATTCCTGGGATGAAG

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
|||| |   || | |  |    |    ||    |   | ||   |  || ||    | |  | | || |  |  ||      | ||  ||| ||  || ||||| || |||||||||||||| ||| |||||||||||||||||||||| || || ||| | |||||||||||||||||||||||||||
gtaa-tgtctaatacaaatgtccatcagttctctggctatttc-tctacatgtggatccattgtaattcagtggta-tgatttctttgctttttgcagACTCCTCTCCATTGCAGAGGAGACTTTGGCAGAGTTCCTCTCAAAGGCTACAGGAACTGCTGTCGATTGGGTCCAGATGCCTGGGATGAAG

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|29634707|gb|CB639716.1|CB639716
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|29642722|gb|CB647729.1|CB647729
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|58663402|gb|CK052088.1|CK052088
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTA
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagG-CTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTA
EST: gi|88205580|gb|CI205429.1|CI205429
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|29678474|gb|CB674749.1|CB674749
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
                            tcttaac  putative branch site (score: 2)
                                     ccttttatcttgttct  putative PPT
                                       ttttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG