Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatcttattgaaggattaatcactaatcattacttcctactctgtaaattagagcggtctagtgtgaacttttgtttgtttcttcactcagtcttt...

Basic information

species Oryza sativa
transcript LOC_Os01g21180.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G180990_T02 (Zea mays), 5'ss of exon 6
GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatcttat-tgaaggattaatcactaatcattacttcctactct--gtaa-attagagcggtctagtgtgaacttttgtttgtttcttcactcagtcttt
||||||||||||||||| ||||| || ||  ||||||||||||||||||||||||||||||| |||||||||| |    | ||||| ||| || | || |    |||     |||   |||| | |  |       ||  || |||  || | || ||  |||||  |    
GCTATAATGGCTGAAGGAAAACAACACGCCCTGGCAATTGGATATACAAAGATGTCAGCAAAAGACATgtaagtttcactctgaagtattgattaata-ttggcactcaagtctcgaagtaatactccaagcacaaagcctgcactcatgctcgtctccgcactctttt---

upper sequence: LOC_Os01g21180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G41130.1 (Glycine max), 5'ss of exon 5
GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatcttattgaaggattaatcactaatcattacttcctactctgtaaattagagcggtctagtgtgaacttttgtttgtttcttcactcagtcttt
|| || ||||||||||| |||||||||||  | || ||||| | |||||| ||||||||||| |||||||||||   |         | |     | |           |  |   | || || |   |  |  | | |    |     |   ||        | || 
GCCATCATGGCTGAAGGAAAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaacttgcattatctcatcttttgactggacaggaatgttgaatgaaataaatatgaattttttcactaataagcagagactctgtcagatattc

upper sequence: LOC_Os01g21180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G13720.1 (Glycine max), 5'ss of exon 6
GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaaga---tcttattgaaggat--taatcactaatcattacttcctactctg-taaattagagcggtctagtgtgaacttttgtttgtttcttcactcagtcttt
|| || ||||||||||| |||||||||||  | || ||||| | |||||| ||||| ||||| |||||||||||   |  ||||     ||  |  | | |   ||  | |    | |    |||||  ||   |||     | |||      |   |     ||||       
GCCATCATGGCTGAAGGTAAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCTGCAAAAGACATgtaagaaacttgtattatctcatcttttttattgggcaggaatgttgaatgaaataaatatgaattgtcactaataaacagagactctgtcagatactcc------

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|88524395|gb|CI452304.1|CI452304
EST:     GGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: GGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88831835|gb|CI369517.1|CI369517
EST:     AAACAGCATGCATTGGCAATT-GATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTTACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88552046|gb|CI482158.1|CI482158
EST:     GATGTCAGCCAAGGACAT                         TAAGACTATCCACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: GATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88511837|gb|CI439343.1|CI439343
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88661141|gb|CI451114.1|CI451114
EST:     ATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: ATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|29289887|gb|CB483501.1|CB483501
EST:     AAACAGCAAGCATTGGC-ATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGAC-ATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88835943|gb|CI371048.1|CI371048
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88529774|gb|CI458120.1|CI458120
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|29687412|gb|CB683687.1|CB683687
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88381483|gb|CI528463.1|CI528463
EST:     TGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: TGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|33682858|gb|CF311097.1|CF311097
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88473032|gb|CI410303.1|CI410303
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88469391|gb|CI406662.1|CI406662
EST:     ATTGGCNATTGGATATACAAAGATGTCAGCCAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: ATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88531796|gb|CI460307.1|CI460307
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88542015|gb|CI471322.1|CI471322
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|218488231|gb|FG951457.1|FG951457
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|3763091|gb|AU029843.1|AU029843
EST:     AACCAGCATGCATTGGCAATTGGATATCCAAAGATGTCAGCAAAGGCCAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|33688444|gb|CF316683.1|CF316683
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|55410731|gb|CV723107.1|CV723107
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88414188|gb|CI533558.1|CI533558
EST:     TACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: TACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88296856|gb|CI540208.1|CI540208
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88852472|gb|CI374240.1|CI374240
EST:     AAACAGCATGCATT-GCAATTGGATATACAAAGATGTCAGCAAA-GACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|86522655|gb|CI162861.1|CI162861
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88506057|gb|CI433563.1|CI433563
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88541753|gb|CI471041.1|CI471041
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88514235|gb|CI441741.1|CI441741
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|58030638|gb|CX728181.1|CX728181
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88508109|gb|CI435615.1|CI435615
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|89196306|gb|CI397308.1|CI397308
EST:     GCAATTGGATATACAAAGATGTCACGCAAAGGACAT                         TAAGACTATCAACAAAGG-ATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: GCAATTGGATATACAAAGATGTCA-GCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88549468|gb|CI479359.1|CI479359
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88283934|gb|CI405380.1|CI405380
EST:     ANACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88534347|gb|CI463065.1|CI463065
EST:     GATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: GATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88531245|gb|CI459707.1|CI459707
EST:     AAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|55410246|gb|CV722622.1|CV722622
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88480133|gb|CI417404.1|CI417404
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88297527|gb|CI550590.1|CI550590
EST:     ATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: ATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
EST: gi|88484301|gb|CI421572.1|CI421572
EST:     AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT                         TAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA
genomic: AAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatctt ... aattttgtagTAAGACTATCAACAAAGGAATTGGAGTTGACAATATGCACTATCTAAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACATgtaagatcttattgaaggattaatcactaatcattacttcctactctgtaaattagagcggtctagtgtgaacttttgtttgtttcttcactcagtcttt

- - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG