Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgcctgtttcctcatcaattgttctttgtgctcgctggcatacttgaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068193_T02 (Zea mays), 3'ss of exon 4
gtactgtgcctgtttcctcatcaattgttctttgtgctcgctggcatacttgaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttc-cagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
           ||  |    || |||| |     || |  | |  |  || |  | || |    ||       ||  || |||  |||||| ||  | ||    ||||||||| ||||||||||| || || || |||||||| ||  ||||||| || |||||||||||||||||||||||||| ||  ||||  |||||| ||||
-----------gtaacacagtccattgct-----tgtttaccgaaactctcggtgtgtgtctctgtac-----tgacggcgatccatcttgcttcctgggacggcagGTTGCTTGGCACCCCAAACGAACAGGTGTGGCCAGGCGTCGGCAAGCTGCCCAACTGGCACGAGTACCCCCAGTGGAAGCCGACGAAGCTGTCTGCTCTT

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 6
gtactgtgcctgtttcctcatcaattgttctttgtgctcgc-tggcatacttgaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
           |||   | |   || |      ||  | || || |    |||| |  | |   | | |    ||     | |  | | ||     ||| | | |||||| ||||||||||| |||||  |  | |||||||||||||  || ||||| |||||||| |||| |||||||||||  ||     |     || |   |
-----------gttcagtga--gatgggatccagttttggcatgtccagtttgatgtatcttcccctctgcctatcaatttaacctttttttgggattttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACCAAACTGGCATGAGTTCCCCCAGTGGAGCCCAAATCAGAATCCTAAGAAT

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ19614 (Selaginella moellendorffii), 3'ss of exon 6
gtactgtgcctgtttcctcatcaattgttctttgtgctcgctggcatacttgaggggtataatcgtgtattc--atggtggtgatttatcttgattgtttggttcca--gGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
                                                 |||  | |||| |  || |  |   | | | ||  ||| | ||  ||| || ||   |  || | ||||| || || || ||  || | ||||| |||||||||||||| | | |||||||||||| ||| |||||||| ||    ||  |          
------------------------------------------------gttgttgtgtatcactgttttcttgaacgtttgtttttttttttttttgcttcgtcataaagGCTCCTGGGTACTCCGAACGATGAAATCTGGCCGGGAGTGAGCAAGCTCCGTGACTGGCACGAGTTCCCGCAGTGGAAACCACAAAACATAAGCCGCGCC

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ06603 (Selaginella moellendorffii), 3'ss of exon 6
gtactgtgcctgtttcctcatcaattgttctttgtgctcgctggcatacttgaggggtataatcgtgtattcatgg---tggtgatttatcttgattgtttggttcca--gGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
                                                 |||  | |||| |  || |  |        || || ||| | ||  ||| || ||   |  || | ||||| || || || ||  || | ||||| |||||||||||||| | | |||||||||||| ||| |||||||| ||    ||  |          
------------------------------------------------gttgttgtgtatcactgttttcttgaacgtttgttgtttttttttttttgcttcgtcataaagGCTCCTGGGTACTCCGAACGATGAAATCTGGCCGGGAGTGAGCAAGCTCCGTGACTGGCACGAGTTCCCGCAGTGGAAACCACAAAACATAAGCCGCGCC

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|29663133|gb|CB659408.1|CB659408
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|29663132|gb|CB659407.1|CB659407
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACC
EST: gi|58604123|gb|CK014651.1|CK014651
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|33801905|gb|CF326824.1|CF326824
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTCCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|89175978|gb|CI042999.1|CI042999
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|86421815|gb|CI059388.1|CI059388
EST:     CAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|58658042|gb|CK046722.1|CK046722
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|88962742|gb|CI023842.1|CI023842
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|86496840|gb|CI139473.1|CI139473
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|86593618|gb|CI264497.1|CI264497
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|88850591|gb|CI094856.1|CI094856
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|58603848|gb|CK014376.1|CK014376
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
EST: gi|88975465|gb|CI023716.1|CI023716
EST:     CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA                         GTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC
genomic: CCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAAgtactgtgcc ... ttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
                                   tcttgat  putative branch site (score: 4)
                              atttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtgcctgtttcctcatcaattgttctttgtgctcgctggcatacttgaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA