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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgcattatcattcgccattgtagatatgtaatgcgaattggcagctatttgtatggtagtttctatttggagggacttcaattatcactcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g38620.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 4
attgcattatcattcgccattgtagatatgtaatgcgaattggcagctatt-tgtatggtagtttctatttggagggacttcaattatcactcttgtg--cagATCGCTTATTCTCTGTTAGA------GGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACA------TATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG
  ||   || |  | || |  | || | | |   |     ||   | || | ||  |  |  |  | |    ||  | ||| |||||| | | |||||  ||||| |||||||||||| ||||      |||||||||||| |||||||    ||  ||||| ||||      |||||||||||||||| |||||||||   |         
--tggcgtaccccttgctagag-agctctctgtagtactatgtaggatactgtggttattcttaacaagaaagaaaggcttaaattattattattgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAAC---------
















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|218487804|gb|FG952787.1|FG952787
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|58594793|gb|CF993101.1|CF993101
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAACAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|27577389|gb|CB000084.1|CB000084
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|218504651|gb|FG960768.1|FG960768
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|33795398|gb|CF323569.1|CF323569
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|38472674|gb|CF956806.1|CF956806
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|86908033|gb|CI298799.1|CI298799
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|27577966|gb|CB000661.1|CB000661
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|218495275|gb|FG966279.1|FG966279
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|218500721|gb|FG955417.1|FG955417
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|33793613|gb|CF322690.1|CF322690
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|38473357|gb|CF957489.1|CF957489
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|38478638|gb|CF962771.1|CF962771
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|58588638|gb|CF986946.1|CF986946
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|313080792|gb|HO213589.1|HO213589
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|27577933|gb|CB000628.1|CB000628
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|58598824|gb|CK009352.1|CK009352
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|218483500|gb|FG948234.1|FG948234
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|25801465|gb|CA757426.1|CA757426
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
EST: gi|218502513|gb|FG958404.1|FG958404
EST:     CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG                         ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT
genomic: CTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagca ... tcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatttgtatggtagtttctatttggagggacttcaattatcactcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG
                                         tcactctt  CT-rich tract
                tttctattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgcattatcattcgccattgtagatatgtaatgcgaattggcagctatttgtatggtagtttctatttggagggacttcaattatcactcttgtgcagATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT