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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaataattgggtcttaaaaaaattgctatttgttttgattttatagtaacattaattaggccaagcttgtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 7
gtgaataattgggtcttaaaaaaattgctatttgttttgattttatagtaacattaattaggccaagcttgtct---tttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC
|||  | ||| |  |||      | ||   | | |  |  | |||     |  |||||||  ||||| |||  |   ||||||||||||||||||||||||||||||||||||||||| || ||||| ||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||
gtgctttatttgtccttttctttaatgtgttgtctggtattgttaagagtatgttaattaaaccaagtttggataattttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCCTTAGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGC

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 7
gtgaataattggg-----tcttaaaaaaattgctatttgttttgatt-ttatagtaacattaattaggccaagcttg---tcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC
|||  | ||| |      |||| ||    |||     | |  |  || |||     |  |||||||  ||||| |||   | |||| |||||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||
gtgctttatttgtccttttctttaatgtgttgtcccctatcctatttgttaagagtatgttaattaaaccaagtttggattatttttagAGAGAGTACGAGGAATTCAAGGTCAGAATCAATGCCTTGGTTGCTAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGC

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 7
----------gtgaataattgggtc---ttaaaaaaattgctatttgttttgattttatagtaacat----taa-----ttaggccaagcttgtctttt----------cagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC
          || ||| | || ||    || |    | ||   ||    |  ||  |  | |  | |    | |     ||  |   |   |||  |||          |||||||| |||||||||||||| ||  | |||||||| |||||||| || || || || || || || ||||| ||||||||||| ||||| ||||| ||||
gtaatgggttgttaatcactgagttgagttgattctactgtccttcacctccatccttcattggcttgtcttgaggattttgtgtttactctgttatttattgagattacagAGAGAATATGAGGAATTCAAAGTTCGGATCAATGCTTTGGTTGCCAAGGCACAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACTCCATGGC

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
-----------------gtgaataattgggtcttaaaaaaattgctatttgttttgattttatag-taacatt---aattaggccaagcttgtctttt-cagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC
                 ||||   | || ||   |   | | |   ||||    ||  || || | | ||| |   |||          ||||||||| |||||||||||||||||||| || ||  | || ||||| |||||||| |||||||| || || || || ||||| ||||||||||| ||||| || || ||||
agactggcttgtgaattgtgatacagtgtgtaccatctacact--cattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC

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|33678973|gb|CF307212.1|CF307212
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|572255|gb|D41766.1|D41766
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|58657578|gb|CK046258.1|CK046258
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|29624917|gb|CB629928.1|CB629928
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|58693391|gb|CK082078.1|CK082078
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|701331|gb|D47622.1|D47622
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|29635077|gb|CB640086.1|CB640086
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|29632077|gb|CB637086.1|CB637086
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|29674793|gb|CB671068.1|CB671068
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
EST: gi|29634895|gb|CB639904.1|CB639904
EST:     TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAG                         AGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT
genomic: TGAAGGATAAGGTGGCACCATACTTTGTTAGGGAGAGGAGAGCAATGAAGgtgaataatt ... gtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatttgttttgattttatagtaacattaattaggccaagcttgtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC
                                          cttgtcttttc  CT-rich tract
     tttgttttgattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaataattgggtcttaaaaaaattgctatttgttttgattttatagtaacattaattaggccaagcttgtcttttcagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA