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

gtatgttgaatgctaattgtgttattaaatcactatattttgtaggaaacatatgtgatggatcaccttcaaagtccatctctctggattttgtagcttttcttttaaaagtagttctttttttttaatctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGATATCTATTAATGATCTAGTTATAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g22720.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 11
gtatgttgaatgctaattgtgttattaaatcactatattttgtaggaaacatatgtgatggatcaccttcaaagtccatctctctggattttgtagcttttcttttaaaagtagttctttttttttaatctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGATATCTATTAATGATCTAGTTATAAAG
                 | ||||  |||   | | | |  | ||  |  | | | || |||   ||    |      ||  || |     || || || |   ||          | |   | | ||||| |   |||||||||||| |||||||| ||| |||||||  | || ||||| ||||| ||||| ||||||||||| || || |||
----------------gtatgtttctaacctaatttgtgatctacaagccctttttgttggtgaac----agcactgattcctttattacttctaactatgagttccttg-----tgtcactctctaatcaa---cagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 7
gtatgttgaatgctaattgtgttattaaatcactatattttgtaggaaacatatgtgatggatcaccttcaaagtccatctctctggattttgtagcttttcttttaaaagt-agttctttttttttaatctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGATATCTATTAATGATCTAGTTATAAAG
                                         ||| |   |  |  | ||  || |  | || ||  | | ||  |||    ||   |    ||| |||   | |||| | |  || ||||| |   |||||||||||| |||||||||||| |||||||  | || ||||| ||||| |||||||| |||||||| || || |||
-----------------------------------------gtatgtttctaacctaatatatgatttacagagctcttttcgttgg----tgggacagcacttctaactttgagttgtgtcattctaatcca---cagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCTATCAATGATCTTGTCATCAAG
















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|58680453|gb|CK069140.1|CK069140
EST:     ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAA                         GTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT
genomic: ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAAgtatgttgaa ... tctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT
EST: gi|58652754|gb|CK041434.1|CK041434
EST:     ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAA                         GTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT
genomic: ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAAgtatgttgaa ... tctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT
EST: gi|55410697|gb|CV723073.1|CV723073
EST:     ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAA                         GTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT
genomic: ATTCCACATTATTACCTGACAGTTGACACACGTGTTGATAATCTCATCAAgtatgttgaa ... tctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggattttgtagcttttcttttaaaagtagttctttttttttaatctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGATATCTATTAATGATCTAGTTATAAAG
                                            atctaat  putative branch site (score: 3)
                               ttctttttttttaatc  CT-rich tract
              ttttcttttaaaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgaatgctaattgtgttattaaatcactatattttgtaggaaacatatgtgatggatcaccttcaaagtccatctctctggattttgtagcttttcttttaaaagtagttctttttttttaatctaatgcagGTTGCGAGGGGAACTGAATCCATTGCAGGAGTCCTCCGGTGGTAAGAAGATATCTATTAATGATCTAGTTATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG