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

AAAGAAAGGAGTTTATTGCTTCGCTGCACAAGAGGAAAACAGAATTATTCATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatattttacatgaatttggactttagcaacttaatgcacttcaaaagttctaacacttcgatatcctgctttgctactttaatacaagtcagtta...

Basic information

species Oryza sativa
transcript LOC_Os03g36750.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 3
AAAGAAAGGAGTTTATTGCTTCGCTGCACAAGAGGAAAACAGAATTATTCATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatattttacatgaatttggactttagcaacttaa-tgcacttcaaaagttctaaca--cttcgatatcctgctttgctactt--taatacaagtcagtta
||||||||||||| || ||||| || ||||||||||||||||||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||||||| ||||||   |    | | ||| ||| ||| |||| | || || ||| |  |  | |  ||  || || | |   |  | |||  |  |  ||   ||   
AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtca-atatttgcaacagctattgacctta-caatttaactacagtttaaatgaacctataaactgtgacattcagaaatatttcttgctgcttgaaacaag---
















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|33684374|gb|CF312613.1|CF312613
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|58609297|gb|CK037330.1|CK037330
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAG
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAG
EST: gi|29625469|gb|CB630480.1|CB630480
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|38473540|gb|CF957672.1|CF957672
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|33797557|gb|CF324638.1|CF324638
EST:     AGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: AGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|117242305|gb|CT842941.1|CT842941
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|58589895|gb|CF988203.1|CF988203
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGGGGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|29657434|gb|CB653709.1|CB653709
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|29657435|gb|CB653710.1|CB653710
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
EST: gi|58586453|gb|CF984761.1|CF984761
EST:     ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAG                         GTTAATAGATGAAGCGCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC
genomic: ATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTAC

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: 74 (upstream exon), 67 (downstream exon)
Score: 40

AAAGAAAGGAGTTTATTGCTTCGCTGCACAAGAGGAAAACAGAATTATTCATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatatt ... caatttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTACTTCAAATGAGAAAGCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAAAGGAGTTTATTGCTTCGCTGCACAAGAGGAAAACAGAATTATTCATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatattttacatgaatttggactttagcaacttaatgcacttcaaaagttctaacacttcgatatcctgctttgctactttaatacaagtcagtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT