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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcatttaaactattgttttcgcttagttctgatgggatgatgtgtgtggctttgttttgaacacacgttggcagcatatgtgctaatcattgtggcaaagacatgctactttgatctgttgtgattttgtttgattcaattattgtatgagaagacaataagcatttgtataatactatttcattgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 15
gtcatcatttaaactattgttttcgcttagttctgatgggatgatgtgtgtggctttgttttgaacacacgttggcagcatatgtgctaatcattgtggcaaagacatgcta-ctttgatctgttgtgattttgtttgattcaattattg-----tatgagaagacaataagcatttgtataatactatt--tcattgtt--cacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
                   ||  |  |||  | ||||    |  ||||  | | |||    |||| || | ||      ||   |  | ||  |  |||  | |  |  ||  |  | || || | || |  |   | |   ||||  ||     ||  ||||||||| ||| ||| || | |||  |||   ||| |||    ||||||||||||||| ||||||||    ||||| |||||||||||||||||||
------------gtaggcattggcatttaact-tgat----tcttgtgcttagatttag--tgaaaactcttt------atgcttcttgattgtcatggatatgctactctgtcccttatttggt-tgttgctacataacataattggtggtcgatacaagaagacaagaagtatt-gtttgatataattatccatggttgttgcagGTTCTATGCTGCAGAAGTGGTCACAGCACTTGAATACCTACATTGCCAAG
















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|66913937|gb|CX100785.1|CX100785
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|86908120|gb|CI300633.1|CI300633
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAAAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|87007902|gb|CI296880.1|CI296880
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|27334351|gb|CA882802.1|CA882802
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     TGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: TGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAG                         GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
genomic: GTGCTTCTAGATAATCAACCTCTGAAGGTTCTACATGAAGATGCAGTCAGgtcatcattt ... ttgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattgtatgagaagacaataagcatttgtataatactatttcattgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG
                                        tttcatt  CT-rich tract
                         atttgtataatactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatcatttaaactattgttttcgcttagttctgatgggatgatgtgtgtggctttgttttgaacacacgttggcagcatatgtgctaatcattgtggcaaagacatgctactttgatctgttgtgattttgtttgattcaattattgtatgagaagacaataagcatttgtataatactatttcattgttcacagGTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC