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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgccctcagttcaggatgtgctgctatattatatctatgtagaagagatccatagtctatctactctcattaatgtcgtcttaattttccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGGCAGACAGGAATACTAGCCTACATTCCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 17
gttagtgccctcagttcaggatgtgctgctatattatatctatgtagaagagatccatagtctatctact-ctcattaatgtcgtc-ttaattttccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGGCAGACAGGAATACTAGCCTACATTCCCAG
|||||| ||||  ||| ||  |  ||||||    | |  ||||  |  |  |    ||  ||| || ||| ||  || |  || |  ||  || ||  ||| ||||||||||||||||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||| ||
gttagttccctt-gttgagcctaagctgct-cggtgtgactattcattacgggctgattttctgtccactgcttgttcagatctttatttcttctctcttttcagTTTATTGATGAAGCATGCCATCAAATTGAGCGTAACGAAAGAAATGTGCGGCAAACTGGAATTCTAGCCTACATTCCAAG
















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|66921504|gb|CX108352.1|CX108352
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
EST: gi|58665096|gb|CK053782.1|CK053782
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
EST: gi|58602109|gb|CK012637.1|CK012637
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAG
EST: gi|58680504|gb|CK069191.1|CK069191
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
EST: gi|58604329|gb|CK014857.1|CK014857
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
EST: gi|29627167|gb|CB632178.1|CB632178
EST:     GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGG                         TTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG
genomic: GCAGACTACTTCATGACTTGGAGTCAAGAATATCAACACAGTTCAGCAGGgttagtgccc ... ccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagatccatagtctatctactctcattaatgtcgtcttaattttccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGGCAGACAGGAATACTAGCCTACATTCCCAG
                                   tcttaat  putative branch site (score: 3)
                                         ttttccatttcc  CT-rich tract
                                     ttaattttccattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgccctcagttcaggatgtgctgctatattatatctatgtagaagagatccatagtctatctactctcattaatgtcgtcttaattttccatttccagTTTATTGATGAAGCGTGCCATCAAATCGAGCGCAATGAAAGAAATGTACGGCAGACAGGAATACTAGCCTACATTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA