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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccattgttgtatcttcattagaagacatcttctggttgagtttgcctaatgattaatttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 5
gtatgccattgttgtatctt-cattagaagacatcttctggttgagtttgc-ctaatgattaatt--tgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA
||||||   || | |||||| |||| ||  | ||  |     ||||||    ||   |  |  |   |||  ||||||||| |||||||||||||| |||||||| || ||||| |||||||| ||||||||| |||||||||| || ||||||||||| ||||| ||||||||
gtatgctgctggtttatctttcatttgagaatattgttccactgagttcattcttgaggctgttcaatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------gtatgccattgtt-gtatcttcattagaagacatcttctgg-----ttgagtttgcctaatgattaatttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA
                              || |    || ||   || ||  ||     |  | |||        ||  |  ||  |  |  ||  ||  | |||||||| | || ||||| |  ||||  |||||    || || |||||||| ||      | | ||||||||  ||||||| ||||||||||||||||||||
gtaattaactgaaacctatttttgtttcatgttttttgtttttcaaattttttttccttaattttttcaaaattttttatgcctgtatcttatttggttgattcagGTGAGGTTATTAGTGAGAGAGATAGGTGCCCCCAGTGCAAAGGAAACAAGGTTAGTACGGAAAAGAAGGTACTGGAGGTGCATGTTGAGAAGGGAATGCA
















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|218492553|gb|FG956401.1|FG956401
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|29665502|gb|CB661777.1|CB661777
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218503180|gb|FG945924.1|FG945924
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58667485|gb|CK056171.1|CK056171
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218484817|gb|FG946762.1|FG946762
EST:     CCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: CCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58603501|gb|CK014029.1|CK014029
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218485257|gb|FG950272.1|FG950272
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58597866|gb|CK008394.1|CK008394
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGA
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGA
EST: gi|29627563|gb|CB632574.1|CB632574
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAC                         GTGAGATGATAAGTGACA
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACA
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     TGGCATGATCCAACAGATGAACACTGTATGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGACACACAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCG
EST: gi|218482248|gb|FG968976.1|FG968976
EST:     AACACTGTTTGCCCTGNAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: AACACTGTTTGCCCTG-AATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58604823|gb|CK015351.1|CK015351
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|13420811|gb|AU174901.1|AU174901
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|29686472|gb|CB682747.1|CB682747
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|116875639|gb|EC366147.1|EC366147
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|3763799|gb|AU030551.1|AU030551
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218499207|gb|FG956931.1|FG956931
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcattagaagacatcttctggttgagtttgcctaatgattaatttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA
                                        gattaat  putative branch site (score: 3)
                                              tttgtcc  CT-rich tract
                                    taatgattaatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccattgttgtatcttcattagaagacatcttctggttgagtttgcctaatgattaatttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG