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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGCTCAATTTCAGAACCAAAATGGCGTCTGGAATATTTTTGGTGGACGCCTTAACTGGGATGATCGAGCAGTTGTTGCAGATGATCCACATTTCCAGgtgaggttccaccttcccttgcaaactatttaattagaattatttgaaaatgtcattcatgaatgttcattatgttaactaagtatcacaacattatgat...

Basic information

species Oryza sativa
transcript LOC_Os01g51754.1
intron # 6
splice site 5'
intron type U2

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|88670301|gb|CI724417.1|CI724417
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88675620|gb|CI729733.1|CI729733
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88665450|gb|CI715606.1|CI715606
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88670102|gb|CI724218.1|CI724218
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|29678996|gb|CB675271.1|CB675271
EST:     GCCTTAACTGGGATGATCGAGCAGTTGTTGCAGATGATCCACATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: GCCTTAACTGGGATGATCGAGCAGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88675813|gb|CI729385.1|CI729385
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88671942|gb|CI726050.1|CI726050
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88688023|gb|CI731599.1|CI731599
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88674847|gb|CI728960.1|CI728960
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88955041|gb|CI720341.1|CI720341
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88672210|gb|CI726326.1|CI726326
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88665561|gb|CI715717.1|CI715717
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|89171865|gb|CI720924.1|CI720924
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88674978|gb|CI729091.1|CI729091
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88675282|gb|CI728501.1|CI728501
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|89172543|gb|CI721602.1|CI721602
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88670475|gb|CI724591.1|CI724591
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88675300|gb|CI728519.1|CI728519
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88972552|gb|CI717292.1|CI717292
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88675071|gb|CI729184.1|CI729184
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88672026|gb|CI726142.1|CI726142
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88973321|gb|CI717795.1|CI717795
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88673010|gb|CI727125.1|CI727125
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88673425|gb|CI727538.1|CI727538
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|89172131|gb|CI721190.1|CI721190
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88666951|gb|CI719087.1|CI719087
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88672542|gb|CI726658.1|CI726658
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88908890|gb|CI716615.1|CI716615
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88908665|gb|CI713223.1|CI713223
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88671260|gb|CI723180.1|CI723180
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88667110|gb|CI719246.1|CI719246
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88669291|gb|CI719429.1|CI719429
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88666333|gb|CI716489.1|CI716489
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88904868|gb|CI712167.1|CI712167
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88955251|gb|CI721823.1|CI721823
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88665392|gb|CI715548.1|CI715548
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88908570|gb|CI713128.1|CI713128
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88669187|gb|CI720144.1|CI720144
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
EST: gi|88904363|gb|CI711671.1|CI711671
EST:     AGTTGTTGCAGATGATCC-CATTTCCAG                         GGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT
genomic: AGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATT

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: 74 (upstream exon), 45 (downstream exon)
Score: 18

GTGTGCTCAATTTCAGAACCAAAATGGCGTCTGGAATATTTTTGGTGGACGCCTTAACTGGGATGATCGAGCAGTTGTTGCAGATGATCCACATTTCCAGgtgaggttcc ... gtccttgtagGGAAGAGGAAACAAGAGCAGTGGAGATAACTTCCATGCAGCCCCAAACATTGATCACTCGCAAGAGTTTGTGAGGAGTGATCTTAAAGAATGGCTTTGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGCTCAATTTCAGAACCAAAATGGCGTCTGGAATATTTTTGGTGGACGCCTTAACTGGGATGATCGAGCAGTTGTTGCAGATGATCCACATTTCCAGgtgaggttccaccttcccttgcaaactatttaattagaattatttgaaaatgtcattcatgaatgttcattatgttaactaagtatcacaacattatgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttccc