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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaggcaaattcttcaggtttagcagttcacactatcttcagagaagtacaacttttctggactatgattctaactgcttcagcattgctgtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA

Basic information

species Oryza sativa
transcript LOC_Os12g31850.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g31850.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------ccaggcaaattctt-caggtttagcagttcacactatcttcagagaagtaca-acttttctggactatgatt--------ctaactgcttcagcattgct--gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA
                          | ||||  | | ||  |  ||    ||| |  |||         ||      ||| ||| | |   ||         || |    || | | || |   ||  ||||||||| | |||||||||||||| |||||||||||| | |||||||| || ||||| ||||||||  |||  || |||||  |||| |||  |||||||||||
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataa-atcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA

upper sequence: LOC_Os12g31850.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S41_115V6.2 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------ccaggcaaattcttcaggtttagcagttcacactatcttcagagaagtacaacttttctggactatgattcta----actgcttcagcattgctgtttcat----cagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA
                                         |||  ||   |  | | || |   |  |    |||  |   ||||      | || | ||     ||   |    |||| || |  | || | |||  |     |||| |||||||||||||||||||||||||| ||| |  | ||   ||| |||   | ||||||| | |  |||||| |  || | | |   |||||| | |
gtttgcaaaaacctaaacttttgctcaatatttttgttgtgaggtgaaca-tgaaagcttggatatgaatgtgatcacctttgaagatt--ttattatagatacccatctaagaggactgtttgaaaactgtttttttgtgtgatagGCGTTGCCACTTGTGAGCACATTCTGGGGCATATTGGTATTCAAGGAATACTACAGATCGTCGAGGAGAACGTATGTTTTGTTGGTGGCGATGCTGGTGA
















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|88972025|gb|CI018491.1|CI018491
EST:     AGTTCATGGGTGTTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|86435471|gb|CI106704.1|CI106704
EST:     GCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: GCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|86491003|gb|CI133636.1|CI133636
EST:     CTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: CTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|33663042|gb|CF294009.1|CF294009
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|58690012|gb|CK078699.1|CK078699
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|89175612|gb|CI042633.1|CI042633
EST:     GCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTA
genomic: GCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTT-GTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTA
EST: gi|29686849|gb|CB683124.1|CB683124
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|88248806|gb|CI247890.1|CI247890
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29644126|gb|CB649133.1|CB649133
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29614659|gb|CB619672.1|CB619672
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29644127|gb|CB649134.1|CB649134
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGTTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29614657|gb|CB619670.1|CB619670
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29616336|gb|CB621348.1|CB621348
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29616334|gb|CB621346.1|CB621346
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|3766608|gb|AU030718.1|AU030718
EST:     AGTTCATGGGTGNTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29670769|gb|CB667044.1|CB667044
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|88224848|gb|CI224370.1|CI224370
EST:     TTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: TTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|58692197|gb|CK080884.1|CK080884
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|58692029|gb|CK080716.1|CK080716
EST:     AGTTCATGGGTGTTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|89184030|gb|CI046595.1|CI046595
EST:     GCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: GCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|88840066|gb|CI079520.1|CI079520
EST:     TGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: TGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29665275|gb|CB661550.1|CB661550
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29669404|gb|CB665679.1|CB665679
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|88274779|gb|CI395185.1|CI395185
EST:     GATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: GATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|89177386|gb|CI250835.1|CI250835
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|86259161|gb|CI010462.1|CI010462
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|88248216|gb|CI248065.1|CI248065
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|86497966|gb|CI140599.1|CI140599
EST:     GGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: GGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|29676246|gb|CB672521.1|CB672521
EST:     AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: AGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
EST: gi|89184119|gb|CI046684.1|CI046684
EST:     GCTATGCTGCTGCTGATGCTGTCCAG                         GCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC
genomic: GCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTAC

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: 49 (upstream exon), 73 (downstream exon)
Score: 14

GCAGTGGGCTCTCCTGGCTGGCTTCCTATGTGGCTTTGGCAATGGGTTTCAGTTCATGGGTGGTCAGGCTGCTGGCTATGCTGCTGCTGATGCTGTCCAGgttagtccaa ... gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtacaacttttctggactatgattctaactgcttcagcattgctgtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA
                       ttctaac  putative branch site (score: 14)
                                           ctgtttc  putative PPT
     aactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaggcaaattcttcaggtttagcagttcacactatcttcagagaagtacaacttttctggactatgattctaactgcttcagcattgctgtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT