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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaatttttcctttcgcctgctgatggtggtgggtgcactggggttgtgattgaacttggtggctggtgatggcag

Basic information

species Oryza sativa
transcript LOC_Os05g29860.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29860.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G042027_T02 (Zea mays), 5'ss of exon 12
GGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgta--gcaaaatttttcc-------tttcgcctgctgatggtggtgggtg-cactggggt-tgtgattgaacttggtggctggtgatggcag--------------------------------------------------------------------
|||  || |||||| ||| | |||||||||||||| || ||||||||||| || |||||||| |||  ||||||||||||||||  |||  | || | |       ||  |    || |    |        |||| |  |  || ||   |   |    ||  | || |                                                                       
GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcaccacttgtgcgaacagcttcagttctcttaaaacgaaaaaaaacactagactacgttatgtgaaccgaaaactctttattgtctttaaactgtacataagttttttagattccccattagacaagttttcagtagtgacacatggcatgcag
















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|33681238|gb|CF309477.1|CF309477
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|29675292|gb|CB671567.1|CB671567
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|33653632|gb|CF276246.1|CF276246
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|86535315|gb|CI175521.1|CI175521
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|66915672|gb|CX102520.1|CX102520
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTTTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|33683403|gb|CF311642.1|CF311642
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|88974714|gb|CI023010.1|CI023010
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|86893712|gb|CI314811.1|CI314811
EST:     ACAATCCTGAGGGAGGAA-GACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: ACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|88956821|gb|CI009049.1|CI009049
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|33686569|gb|CF314808.1|CF314808
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|88977074|gb|CI024811.1|CI024811
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
EST: gi|88901491|gb|CI008919.1|CI008919
EST:     GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG                         GGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC
genomic: GCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTC

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: 54 (upstream exon), 49 (downstream exon)
Score: 3

GGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaat ... gtgatggcagGGGATCGAGCCGCGGGTGCTGTGGATTGGCATCGGCGGGTCCATCTTCTTCGGCGTGCTGGAGAAGACCAAGTCGATGCTCGCCGAGAGGAGGAGCCGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgtagcaaaatttttcctttcgcctgctgatggtggtgggtgcactggggttgtgattgaacttggtggctggtgatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG