Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataatcggttgtctgctctagtaat...

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 4
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactg-------gatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataatcggttgtctgctctagtaat
 || |  || |||||||| ||||||||||| ||| |||| || ||||||||||| || ||||||||||||||||||||||||| |||  ||| |||        ||| | ||  | |  | ||| | |  | | |||  |   | || ||    |  || ||      |   |||          
GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattat-cctttgatctgaaatcacctgactc------

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgc-tttataatcggttgtctgctct--agtaat----
||| |  || |||||||| ||||||||||| ||| ||||| | |||||||||||||| |||||||||||||||||||||||||||||  ||| |||  ||     || ||     | ||||  ||     |||   | || || |    | ||||| ||   |  | ||||||  | ||||    
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttctt-----gttc--cctttattgtgtacatttattattcttcctttgctctgaaataatctga

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G431350_T03 (Zea mays), 5'ss of exon 3
----------------------AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgc-tttataatcggttgtctgctct--agtaat----
                      ||| |  || |||||||| ||||||||||| ||| ||||| | |||||||||||||| |||||||||||||||||||||||||||||  ||| |||  ||     || ||     | ||||  ||     |||   | || || |    | ||||| ||   |  | ||||||  | ||||    
TTTCCAATCTTGGTGGTTTCAGAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttctt-----gttc--cctttattgtgtacatttattattcttcctttgctctgaaataatctga

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G883149_T01 (Zea mays), 5'ss of exon 3
----------------------AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactg-------gatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataatcggttgtctgctctagtaat
                       || |  || |||||||| ||||||||||| ||| |||| || ||||||||||| || ||||||||||||||||||||||||| |||  ||| |||        ||| | ||  | |  | ||| | |  | | |||  |   | || ||    |  || ||      |   |||          
TTTCCAACCTTGGTGGTTTCAGGAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattat-cctttgatctgaaatcacctgactc------

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 4
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataat-cggttgtctgctctagtaat-----
|   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| |||||  | |||    |  |  || | ||||    ||||  | |||  |||| ||||||  |        |    || | || |  ||  ||  ||    |||     
AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGGgta--tgctatatgctattcatatgaaat----ttatctccttcagttgtgtgtttgtttgcttctctaaatcttctcatgcacttccctcttcctccaatacaaa

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G02270.3 (Glycine max), 5'ss of exon 4
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggc----tttcatggcacgctttataatcggttgtctgctctagtaat
|   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| |||||     ||  ||      |||  |  | |  |  ||  ||  ||||||  | ||  |    | |  |    |||||   | | |    ||    |||  || 
AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGGgtatgctatatgctattcatatgaaatttatcttctttagttgtgtttgttagcttctcaaaatcttctcttgcgcttcccacttg---ttccaacctacaaa-

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|58696220|gb|CK084907.1|CK084907
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|88983146|gb|CI020710.1|CI020710
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|33688934|gb|CF317173.1|CF317173
EST:     AAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTG
genomic: AAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGA-GGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTG
EST: gi|33692847|gb|CF321086.1|CF321086
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCAC
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagG-ATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCAC
EST: gi|88839775|gb|CI015866.1|CI015866
EST:     GATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|8857691|gb|AU095009.1|AU095009
EST:     AAATCTGGATCTCATCCCTATTTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: AAATCTGGATCTCAT-CCTA-TTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|88541797|gb|CI471090.1|CI471090
EST:     ATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: ATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|33820857|gb|CF336233.1|CF336233
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|163918457|gb|EG713211.1|EG713211
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|33678548|gb|CF306787.1|CF306787
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAA
EST: gi|218500698|gb|FG952590.1|FG952590
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|88531839|gb|CI460354.1|CI460354
EST:     TATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: TATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|58585721|gb|CF984029.1|CF984029
EST:     GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGA
genomic: GAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGA
EST: gi|88383090|gb|CI538118.1|CI538118
EST:     AAATTGTTGATGGAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
genomic: AAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACA
EST: gi|33683273|gb|CF311512.1|CF311512
EST:     AAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAAGG                         GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCAC
genomic: AAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGA-GGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCAC

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: 69 (upstream exon), 71 (downstream exon)
Score: 13

AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatccta ... gattatacagGATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataatcggttgtctgctctagtaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG