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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgactcatcttcatcattatcaatgagtaccatgtttgatgcatcattgacaaccaatttaaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA

Basic information

species Oryza sativa
transcript LOC_Os02g02690.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 8
gtaatttgactcatcttcatcattatcaatgagtaccatgtttga---tgcatcattgacaacca-atttaaactgca---gAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA-
||||| || ||||   |       |  | |       ||||||     |||    |||  ||||    |  | || ||   |||||||||||||||||| ||||| ||||| ||||| || ||||| ||||| |||||||||||||| |||| ||| || | ||||  |||   ||||  || 
gtaatctggctcagtgttgctgccactagtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAG-TCCACATCTGTTGGAGGCCAT
















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|88474110|gb|CI411381.1|CI411381
EST:     TAGGTCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88247791|gb|CI247640.1|CI247640
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|89182448|gb|CI113817.1|CI113817
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88481854|gb|CI419125.1|CI419125
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86428585|gb|CI075266.1|CI075266
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88481007|gb|CI418278.1|CI418278
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86491300|gb|CI133933.1|CI133933
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86426334|gb|CI071431.1|CI071431
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86505602|gb|CI148235.1|CI148235
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88248278|gb|CI248127.1|CI248127
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86501777|gb|CI144410.1|CI144410
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88227499|gb|CI226979.1|CI226979
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88514227|gb|CI441733.1|CI441733
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88477822|gb|CI415093.1|CI415093
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88990699|gb|CI108086.1|CI108086
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|396941424|gb|HO188633.1|HO188633
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88245688|gb|CI245537.1|CI245537
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88974820|gb|CI023114.1|CI023114
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|94362670|gb|CI052789.1|CI052789
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86539112|gb|CI179318.1|CI179318
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|89167956|gb|CI109160.1|CI109160
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|163926568|gb|EG712432.1|EG712432
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88221660|gb|CI221616.1|CI221616
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|88281120|gb|CI402318.1|CI402318
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86503019|gb|CI145652.1|CI145652
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
EST: gi|86426368|gb|CI071465.1|CI071465
EST:     TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG                         AAGCTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG
genomic: TAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAG

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: 48 (upstream exon), 40 (downstream exon)
Score: 5

GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAGgtaatttgac ... taaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatcaatgagtaccatgtttgatgcatcattgacaaccaatttaaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA
                              cattgac  putative branch site (score: 5)
                                         aatttaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgactcatcttcatcattatcaatgagtaccatgtttgatgcatcattgacaaccaatttaaactgcagAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG