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

gttattccatttattctttagtgcattacttgactataaaatctgcttgaggatgtatacaaaataatgagtactacatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGGTGCTCCGAATGCTAAAAGTAGATCAGGGGGAAATGACCCAGATG

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 14
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 14
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 14
gttattccatttattctttagtgcattacttgactataaaatctgcttgaggatg-tatacaaaataatgagtactacatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGGTGCTCCGAATGCTAA---AAGTAGATCAGGGGGAAATGACCCAGATG
|||  ||| ||  ||   |      |  ||  |  |  |  | || ||     || || ||||| ||||   || ||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |||| ||||||||    || | ||| || ||||||||||| |   
gttgctcctttcctttcattaaatgtagctacatgactacctttgtttttatttgatagacaaactaatagctattacctttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCACTTGTTCCAGCTGGTTCTCCTAATGCTAATAAGAGCAAATCCGGAGGAAATGACCCGG---

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 14
gttattccatttattctttagtgcattacttgactataaaatctgcttgaggatgtatacaaaataatgag----------tactacatt-tgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGG---TGCTCCGAATGCTAAAAGTAGATCAGGGGGAAATGACCCAGATG
|| |||   |  |     | ||    |  |||    | | ||     |||  || | ||| |||| || |           | || |||  | ||||||||||||||||| || || ||||||||||| |||||||| |||| |||  ||||   ||||   |||| ||| |  ||          ||||||   ||||
gtcatt--gtcaaccgaatggttttctgtttggtctttagatgcaactgat-atatgtactaaatcatcatgtttcttttttgcttcataatacagAGTTCCTTTTTTGCGCACTTCATGTGCTTTGAGGTACCTGCTCTTGCTCCTCCTGGAGGTGCTGGCAATGATAAGAAAAGCCAGTCCAACAATGAC---GATG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 14
gttattccatttattctttagtgcattacttgactataaaatctgcttgaggatgtatacaaaataatgag----------tactacatt-tgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGG---TGCTCCGAATGCTAAAAGTAGATCAGGGGGAAATGACCCAGATG
|| |||   |  |     |  |   ||  ||| |  | | ||     |||  || | ||| ||||  | |           | || |||  | ||||||||||||||||| || || ||||||||||| |||||||| |||| |||  ||||   ||||   |||| ||| |  ||          ||||||   ||||
gtaatt--gtcaaccgaatgattttttgtttggcctttagatgcaactgat-atatgtactaaatcctcatgtttcttttttgcttcataatacagAGTTCCTTTTTTGCGCACTTCATGTGCTTTGAGGTACCTGCTCTTGCTCCTCCTGGAGGTGCTGGCAATGATAAGAAAAGCCAGTCCAACAATGAC---GATG

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|29645303|gb|CB650310.1|CB650310
EST:     ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAG                         AGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA
genomic: ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAGgttattccat ... acatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA
EST: gi|58654154|gb|CK042834.1|CK042834
EST:     ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAG                         AGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA
genomic: ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAGgttattccat ... acatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA
EST: gi|58612470|gb|CK040182.1|CK040182
EST:     ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAG                         AGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA
genomic: ATGCATATTCAAAGATGCTAACAATATTTATCCCACTTCTTGTGGATGAGgttattccat ... acatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactataaaatctgcttgaggatgtatacaaaataatgagtactacatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGGTGCTCCGAATGCTAAAAGTAGATCAGGGGGAAATGACCCAGATG
 acttgac  putative branch site (score: 4)
                      atgtatacaaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattccatttattctttagtgcattacttgactataaaatctgcttgaggatgtatacaaaataatgagtactacatttgcagAGTTCCTTTTTTGCACATTTTATGTGCTTTGAAGTACCTGCCCTTGTTCCAGCTGGTGCTCCGAATGCTAAAAGTAGATCAGGGGGAAATGACCCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG