Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGTGCGCCACATTGCTTCATCGACAAATGAAGAAGCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttctcattttactatttcataatcccttctgtggcagtggcactgagtattcctctttgtttattttatggaag

Basic information

species Oryza sativa
transcript LOC_Os06g45660.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G143767_T01 (Zea mays), 5'ss of exon 3
ATTTGTGCGCCACATTGCTTCATCGACAAATGAAGAAGCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttctcattttactatttcataatcccttctgtggcagtggcactgagtattcctctttgtttattttatggaag
 ||||||||||| |||||||||||  |||| || ||||||||||| | |||||| || || || |||||  |||||||||| ||||||||    |  | |  || |    | ||| ||  || |  ||||      | |  | ||     | ||||| |||    |  
GTTTGTGCGCCATATTGCTTCATCATCAAACGAGGAAGCTGCTGCCAGAGCAGCCGCCGCCACTGCTGACGCTGGAGGACCAACCATgtagatatcataaacttgc----ttatactctgttttacggca------ccggatgtttactatcgtttaatttgctcag-
















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|88571508|gb|CI662881.1|CI662881
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|38480548|gb|CF964637.1|CF964637
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATGGCGAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88736487|gb|CI759995.1|CI759995
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|218505045|gb|FG968801.1|FG968801
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88575049|gb|CI666818.1|CI666818
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88572461|gb|CI664032.1|CI664032
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|38477525|gb|CF961658.1|CF961658
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTGGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|58596640|gb|CK007168.1|CK007168
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88347703|gb|CI655056.1|CI655056
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33822248|gb|CF336938.1|CF336938
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|38475488|gb|CF959621.1|CF959621
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|38475613|gb|CF959746.1|CF959746
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGAGGGT                         TTTTGACAAGATCATTGGAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88334078|gb|CI641129.1|CI641129
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33689070|gb|CF317309.1|CF317309
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|25797786|gb|CA753747.1|CA753747
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|55414604|gb|CV726980.1|CV726980
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|55414535|gb|CV726911.1|CV726911
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|38481086|gb|CF965175.1|CF965175
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|163925430|gb|EG713343.1|EG713343
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88382349|gb|CI633207.1|CI633207
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33657720|gb|CF280334.1|CF280334
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|24208483|gb|AU225510.1|AU225510
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTGGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88345287|gb|CI655747.1|CI655747
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88376801|gb|CI639126.1|CI639126
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCCTTCTAATGTTGTCTATGAGG
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCC-TTCTAATGTTGTCTATGAGG
EST: gi|33823879|gb|CF337751.1|CF337751
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33656833|gb|CF279447.1|CF279447
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88380875|gb|CI634900.1|CI634900
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|11442620|gb|BF430523.1|BF430523
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88308825|gb|CI654108.1|CI654108
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTNGTCTATGACGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|55435458|gb|CV730859.1|CV730859
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33815380|gb|CF333544.1|CF333544
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|33659581|gb|CF282194.1|CF282194
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88736146|gb|CI759654.1|CI759654
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88361022|gb|CI646046.1|CI646046
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|112785873|gb|EE591589.1|EE591589
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
EST: gi|88586835|gb|CI704555.1|CI704555
EST:     GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCAT                         TTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA
genomic: GCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGA

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: 57 (upstream exon), 75 (downstream exon)
Score: 26

ATTTGTGCGCCACATTGCTTCATCGACAAATGAAGAAGCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttc ... tttatggaagTTTTGACAAGATCATTGCAAAGGAAATTCCTTCTAATGTTGTCTATGAGGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGTGCGCCACATTGCTTCATCGACAAATGAAGAAGCTGCTGCTAAAGCAGCAGCAGCAACAGCTGATACTGGAGGACCGACCATgtaagctttctcattttactatttcataatcccttctgtggcagtggcactgagtattcctctttgtttattttatggaag

- - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA