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'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   		48  
 5'  3'   		49  
 5'  3'   		50  
 5'  3'   		51  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgccttctgtcatacttgctgttaagctgcacttctaagctttataatctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 51
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 50
gtctgccttctg-tcatacttgctgttaagc-tgcacttctaagctttata--atctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA---
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || |||||   
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTC---ATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 34
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA---
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || |||||   
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTC---ATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 52
gtctgccttctg-tcatacttgctgttaagc-tgcacttctaagctttata--atctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || |||||
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTC---ATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
lower sequence: GRMZM2G009849_T03 (Zea mays), 3'ss of exon 33
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || |||||
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTC---ATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA

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|88328186|gb|CI649997.1|CI649997
EST:     TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
genomic: TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
EST: gi|25807050|gb|CA763011.1|CA763011
EST:     TACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
genomic: TACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         C
genomic: TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcag-
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         C
genomic: TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcag-
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         C
genomic: TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcag-
EST: gi|88381621|gb|CI682287.1|CI682287
EST:     TTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
genomic: TTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
EST: gi|88328663|gb|CI678460.1|CI678460
EST:     TTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
genomic: TTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
EST: gi|29680246|gb|CB676521.1|CB676521
EST:     TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
genomic: TAATAGGTTACAAACTACTAACCTACAGACCGACAGATACCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG
EST: gi|30226797|gb|CB964689.1|CB964689
EST:     CCAATCTTCAG                         GGACGTTGGATGCCCTTAGGGAACGGATGTTAAGCATTCAATCTGCTGCTG
genomic: CCAATCTTCAGgtctgccttc ... atgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacttctaagctttataatctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA
                   atctgat  putative branch site (score: 4)
                                     ttctttctat  putative PPT
             tttataatctgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgccttctgtcatacttgctgttaagctgcacttctaagctttataatctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA