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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacataggttttgagatattccatcagaagttccataacaagttgttacctttgttgaaaatttattgattttttctccttcctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAGCCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 10
gtatgtacataggttttgagatattccatcagaagttc------cataacaagttgttacctttgttgaaaattta--ttgattttttctccttcct---atttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG---------CCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT
|||||||  | ||  ||| || | ||   | ||||||       ||| | ||   ||||   ||| |  |||      |||| ||  ||  | |  |   |||| |||||| ||||||| |||||||| ||| ||||||||||||| ||||||||||||         || ||| ||||||  |||||| | || || || |||||||         
gtatgtagttggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattcttggtagaaaaaagatttgagttcctccacattgtttcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAGAGTGTTGCTCCAACAGCAAACATTGCTGATACAAGAGTATTAGATTATG---------

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 9
gtatgtacataggttttgagatattccatcagaagttc------cataacaagttgttac-ctttgttgaaaatttattgattttttctcc----ttcctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG---------CCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT
        || ||  ||| || | ||   | ||||||       ||| | ||   ||||  |||||| || ||   ||||| |||||| ||    ||   ||||  ||||| ||||||| |||||||||||| |||||||||||||||| |||||||||         || ||| ||||||  |||||| | || ||||| |||||||         
------gtatggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattctttgtagagaaaagattgagtttttcacccattttttcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG---------
















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|88392637|gb|CI625459.1|CI625459
EST:     GTGAAGCCAAGGAATTCTTGCGCACCAGGTTGATTGGGAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: GTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|58658629|gb|CK047309.1|CK047309
EST:     TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|29625604|gb|CB630615.1|CB630615
EST:     TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|29656202|gb|CB652477.1|CB652477
EST:     TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCCA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAACACTGTGGAT
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGAT
EST: gi|58684285|gb|CK072972.1|CK072972
EST:     TGGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|88352099|gb|CI626099.1|CI626099
EST:     GTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: GTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|58606427|gb|CK034460.1|CK034460
EST:     TGGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|29644258|gb|CB649265.1|CB649265
EST:     TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
EST: gi|29623984|gb|CB628995.1|CB628995
EST:     TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAA                         GTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG
genomic: TTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacat ... ctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagttgttacctttgttgaaaatttattgattttttctccttcctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAGCCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT
                          tattgat  putative branch site (score: 3)
                        tttattgattttttct  CT-rich tract
             tttgttgaaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacataggttttgagatattccatcagaagttccataacaagttgttacctttgttgaaaatttattgattttttctccttcctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAGCCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT