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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactacatacattatatcacattaacattcctggtcgcataagattggcctttggtaatgaacatcgctgtaatccttttatcattgcag

Basic information

species Oryza sativa
transcript LOC_Os08g44530.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 13
GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactacatacattatatcacattaacattcctggtcgcataagattggcctttggtaatgaacatcgctgtaatccttttatcattgcag
||| ||||| |||||||| || || |||    |||| |||||||| |||||||||||||| || |||||| ||||| |  || ||||||| |||||||||||||||   |     ||  |     |  |  ||  |||   || |   |||||  |  ||  ||||  || || |  ||| | ||| |||||||
GAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAGAAAGGCGGAGGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc-----ttgaacattgtctatcttgttggcatcagagccttggc--tccgtgctgaatgtctcttt--tccatatattattgcag

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AC234528.1_FGT005 (Zea mays), 5'ss of exon 13
GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactacatacattatatcacattaacattcctggtcgcataagattggcctttggtaatgaac---atcgctgtaatccttttatcattgcag
||| ||||| || ||||| || || ||     |||| ||||||||||||||||||||||| || |||||| ||||| |  || ||||||| |||||||||||||||   | ||         || ||  |     || | |||| ||| |   | ||||    |  |   ||  || |  ||| | ||| |||||||
GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagctta--------aacgttgtctgcgttgttggcatcagagtaatccttggctccgtgctgaatgtctcttctccatgtattattgcag
















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|86413805|gb|CI068012.1|CI068012
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|88830002|gb|CI074674.1|CI074674
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|8858265|gb|AU095583.1|AU095583
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|86255894|gb|CI068343.1|CI068343
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCTCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|88965683|gb|CI006589.1|CI006589
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCCTGCATCAAGAGGATGCGTCACCGATGAGTA
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCC-TGCATCAAGAGGATGCGTCACCGATGAGTA
EST: gi|88971557|gb|CI017871.1|CI017871
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCC-TGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|86823618|gb|CI258691.1|CI258691
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAT-TCGTGTCCC-TGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|86428510|gb|CI075191.1|CI075191
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|86537187|gb|CI177393.1|CI177393
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGATAGCTCGTGTCCCCTGCTATCAAGAGGATGCGTCACCGATGAGT
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGA-AGCTCGTGTCCCCTGC-ATCAAGAGGATGCGTCACCGATGAGT
EST: gi|89180557|gb|CI044836.1|CI044836
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|88848058|gb|CI086580.1|CI086580
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCGCCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|88960472|gb|CI006433.1|CI006433
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
EST: gi|5038803|gb|AU070913.1|AU070913
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGT
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGT
EST: gi|86488131|gb|CI130764.1|CI130764
EST:     GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAG                         TACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG
genomic: GGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAG

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: 58 (upstream exon), 72 (downstream exon)
Score: 12

GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactac ... atcattgcagTACACGAAGCTCGTGTCCCCTGCATCAAGAGGATGCGTCACCGATGAGTAGATCCTGCTGCTGCTGCTCGAGTAATAAAAAATAAAAAATAAAAAAGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactacatacattatatcacattaacattcctggtcgcataagattggcctttggtaatgaacatcgctgtaatccttttatcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG