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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattctccactcacctcgtccatcaataatgtagggtgcatccttggatgaactctagacctggccctttgcggcatactaatttgaacgtaagctgaaaatttgcaaaccacgtccacttttagaatgaaaaattcaactctaatgacataaacttgctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC

Basic information

species Oryza sativa
transcript LOC_Os12g07110.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 11
gtttgtattctccactcacctcgtccatcaataatgtagggtgcatccttggatgaactctagacctggccctttgcggcatactaatttgaacgtaagctgaaaatttgcaaaccacgtccacttttagaatgaaaaattcaactctaatgacataaacttgctattt--cagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC
                                                                      | | || |       || ||| | | | | | ||      |||| |  || |||  |||  |  | || ||  | |  |     ||  ||||| |||||  ||||||||||||||||||||||| |||||||||||||| || | ||| |||||||||||| | |||||||||||||| ||||| || || |||||||||||||
---------------------------------------------------------------------acgtgtgtgctga---aagttgcaagcatg-tcaagcgagacaaatcctgtgcaccgttaagacaacaattttgattgcacccg-atgcacttgttattttccagGCTGCGAAGCAAGCGCGACTTGAGAAGTTTGAGATACCAGTCAAAATCAAGCTGATACCAGAGCCATGGACCCCCGAGTCGGGACTCGTCACTGCTGCCC

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
gtttgtattctccactcacctcgtccatcaataatgtagggtgcatccttggatgaactctagacctggccctttgcggcatactaatttgaacgtaagctgaaaatttgcaaaccacgtccacttttagaatgaaaaattcaactctaatgacataaacttgctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC
                                                                        ||| |  || |   ||| |||  | |  | |      ||||  ||  |  | |||    |  ||   | | ||| |       |    ||  |  | ||||| || ||||| || || |||||||||||||||||||| |||||||||||  || |  ||||  ||||||| || ||  |||| || |||||||| || |
---------------------------------------------------------------------atgtttaca-cacatacattagaaaatgatat-acctgccgcaagtca-atttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
















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|86852155|gb|CI317898.1|CI317898
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTT-GATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACT-GAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|88263749|gb|CI366650.1|CI366650
EST:     TGTGCCAGAAGCCAGAGG-TGTTAAAGAAGTGCTT-GATCTCTATCAAAG                         GCTGCGAACCAAGCGCGACTGGAGAAATTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|88490515|gb|CI427787.1|CI427787
EST:     CAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: CAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|29674410|gb|CB670685.1|CB670685
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|29622299|gb|CB627310.1|CB627310
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|86436734|gb|CI118456.1|CI118456
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|86418620|gb|CI032829.1|CI032829
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|88486659|gb|CI423930.1|CI423930
EST:     GTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: GTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|88506918|gb|CI434424.1|CI434424
EST:     GTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAANTTTGAGATCCCGGCCAAGATCAAG
genomic: GTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|86479777|gb|CI122410.1|CI122410
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
EST: gi|86874630|gb|CI318189.1|CI318189
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAA
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAA-Ggtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAA
EST: gi|89195791|gb|CI007210.1|CI007210
EST:     TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAG                         GCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG
genomic: TGTGCCAGAAGCCAGAGGCTGTTAAAGAAGTGCTTGGATCTCTATCAAAGgtttgtattc ... gctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtccacttttagaatgaaaaattcaactctaatgacataaacttgctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC
                           ctctaat  putative branch site (score: 3)
                                              ctatttc  putative PPT
       ttttagaatgaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtattctccactcacctcgtccatcaataatgtagggtgcatccttggatgaactctagacctggccctttgcggcatactaatttgaacgtaagctgaaaatttgcaaaccacgtccacttttagaatgaaaaattcaactctaatgacataaacttgctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC