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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccattgttgtatcttcattagaagacatcttctggttgagtttgcctaatgattaatttgtccag

Basic information

species Oryza sativa
transcript LOC_Os02g43930.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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
















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|29665502|gb|CB661777.1|CB661777
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     TGGCATGATCCAACAGATGAACACTGTATGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGACACACAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218503180|gb|FG945924.1|FG945924
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|58661241|gb|CK049921.1|CK049921
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58603501|gb|CK014029.1|CK014029
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|58597866|gb|CK008394.1|CK008394
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGA
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGA
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCG
EST: gi|218485257|gb|FG950272.1|FG950272
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
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|29683463|gb|CB679738.1|CB679738
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|29686472|gb|CB682747.1|CB682747
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|218492553|gb|FG956401.1|FG956401
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
EST: gi|116875639|gb|EC366147.1|EC366147
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
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAG                         GTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 250

CATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccatt ... atttgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAGAGGATCAGgtatgccattgttgtatcttcattagaagacatcttctggttgagtttgcctaatgattaatttgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT