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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatgacaacag...

Basic information

species Oryza sativa
transcript LOC_Os02g49980.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G089454_T03 (Zea mays), 5'ss of exon 3
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactg--tatttaattctcaggatgattaaattgggggaagac-acaatacataacctttatgacaacag
|||| ||||||||||| || |||||||||||||||||||| |||||||| |||||||| || |||||||||||||| ||||||||||||||||| || |||||||| ||||| |   |||  || || ||    | ||  ||||| ||  ||||  |  |   | || |  | ||  |||| |  |||| |  |   ||  | 
TCACCAAGGGGAATGTCACAATTAAACTTTGGGATCTTGGTGGGCAACGAAGATTCCGCACTATGTGGGAGCGCTACTGCCGTGGAGTTTCTGCTATTCTgtaatt-cctgctcttctaaaata-ctattcaatattgaatattttatattcagttttttgttagtgagataggattacaacat-taacatacaactcagaat

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 5
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacc-tttatgacaacag--
|||| ||||| ||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||| || |||||||| ||||| |   |||| |||     || |  |  |||| ||  |||   | |   |        ||    |||     | |  ||||||         
TCACCAAGGGAAATGTCACGATTAAGCTTTGGGATCTTGGTGGGCAGCGGAGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaatt-cctgctcttctaagatattaa--atactgtagatttcatattcattgtaacatacaactcataacctccaaattggagcaatttatggttggtatt

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 5'ss of exon 3
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgta-atttcctgcacacttaagctatctgttatg--cactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatgacaacag
| ||||| || |||||||| || ||  |||||||||||||||||||||| || || || ||||||||||| || || || || || ||||| || ||  |||| ||   ||  | ||||   | || |||| ||  ||    || | | | |  || | || ||  |  |     | |   | |        |||  ||    
TTACAAAAGGAAATGTTACAATAAAGATTTGGGATCTTGGAGGGCAACGAAGGTTTCGTACCATGTGGGAACGTTACTGTCGCGGTGTTTCCGCCATTGTgtacatcctcttaaaacttcttcgatatgttttgaacatcccatgttactatttggttaat-aatctttgatggtatatgttgctgtggtaatattgcag---

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 5'ss of exon 5
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgca--cacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatg-acaacag
| |||||||| ||||| |  || ||  ||||||| || |||||||||| ||| || || |||||||||||||| || ||||| || || |||||||| ||||||| ||    |  | ||||| || ||| ||||  |   | | ||    |     ||    |      |     | || | || ||   | ||  ||| |  
TTACAAAGGGAAATGTAATAATAAAGGTTTGGGACCTGGGAGGGCAACAGAGGTTTCGTACCATGTGGGAGCGTTACTGCCGAGGTGTCTCTGCAATTCTgtaatatctccaagcctcttaaactttctcttatctatc-tgtctatgcatgcacgtggcacatacacagattttctcattccagaaaactaattcacatc--

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S103_13V6.1 (Physcomitrella patens), 5'ss of exon 4
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgca----cacttaagctatc-tgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatac---ataacctttatgacaacag------------------------------------------
| || ||||| | ||| || || ||||| |||||||| || || ||||   ||||||||| |||||||||||| ||||| ||||| || ||||||||  |||||    |||      |||  ||| | |  | || |||  ||  | ||| | |  | |  |||   |   |   |    || |      |       ||    | ||                                          
TGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATTGTCGTGGTGTGTCTGCAATTGTgtaagaatctgtgtttccaccaaagttttggttttctgcgatggctctaaatatt-gaagcattttctcacgaccatttgcagtctcctgtggttcaaattttgaaagtatgtattttgaagcatttaggtgacctggtaactgtttcag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ07633 (Selaginella moellendorffii), 5'ss of exon 4
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatgacaacag
| || || || ||||| ||||| || || |||||||| || || ||||   | |||||||  |||||||||||||||||||| |||||||| || ||| |||||   | |     ||  |||   |   |     |      |||      | | |    ||       || | | ||| | |    |||          
TGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATTGCCGCGGAGTTTCAGCTATCGTgtaagaactt-----ctcgagccgccaact---tgcgacgactaac-----gaacgcacgaa------aaaaaaaaaattctttggttttccag------

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ11035 (Selaginella moellendorffii), 5'ss of exon 4
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatgacaacag
| || || || ||||| ||||| || || |||||||| || || ||||   | |||||||  |||||||||||||||||||| |||||||| || ||| |||||   | |     ||  |||   |   |     |      |||      | | |    ||       || | ||  |   |    ||   |       
TGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATTGCCGCGGAGTTTCAGCTATCGTgtaagaactt-----ctcgagccgccaact---tgcgacgactaac-----gaacgcacgaa-----aaaaaaaactttctttggttttccag-------

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|86512088|gb|CI154721.1|CI154721
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|8324374|gb|AU091530.1|AU091530
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|33817712|gb|CF334689.1|CF334689
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88342916|gb|CI640249.1|CI640249
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGAT
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGAT
EST: gi|88575977|gb|CI670122.1|CI670122
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATACCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|33808162|gb|CF329970.1|CF329970
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88345402|gb|CI656060.1|CI656060
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCA
EST: gi|33817714|gb|CF334690.1|CF334690
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|86600191|gb|CI251561.1|CI251561
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|55442549|gb|CV734564.1|CV734564
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|66923097|gb|CX109945.1|CX109945
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAA
EST: gi|86601190|gb|CI251570.1|CI251570
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|58665641|gb|CK054327.1|CK054327
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88347247|gb|CI632532.1|CI632532
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACC
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACC
EST: gi|33818441|gb|CF335055.1|CF335055
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|58586064|gb|CF984372.1|CF984372
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|55414064|gb|CV726440.1|CV726440
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACAAAGGGGAATGTTACGATTAAACTTTGGGATCTTGGAGGGCAACGGAGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcctgcacacttaagctatctgttatgcactgtatttaattctcaggatgattaaattgggggaagacacaatacataacctttatgacaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG