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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG

Basic information

species Oryza sativa
transcript LOC_Os08g10600.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 4
-ttatagag-tatttttggagtaatatcctacgttttagtctgctttcagt-cttcagtga-tcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
 | |   || |    | ||| ||   |   || ||||    | |   ||   || |||  | |||||| | |  |  | | || | ||    |||  |||| ||| |||||||| |||||| | ||||||||||||||||| ||||||||||| ||||| || || |||||||||||||| |||| ||||||||
ttcacttagctgccatgggaatatgttatcactttttgaggttcaaccaaaactccagcaagtcttaatagttttcatttcctctccc----attgttgcttagGTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtct---tcagtgatcttaagattcatggtgttcttttcctctgatttctgctc-agGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
 | ||    | || |||    || |    | ||||| | |||||| ||  |   |||   |    |   ||  |  |||  | ||    |   || |  |  ||  || || |||||||||||||| |||||||| ||||||||||||||  | ||||||||   |||||  || ||||||||  | ||  |||   
-tctaagtaagttgtgg---tatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 5
--ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttca--gtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
  |     ||||  || |  ||| | |  | | ||||| | |||||| ||  |  |   |||  |  |  || ||| | || || |  | | |||     | ||  || || |||||||||||||| |||||||| ||||||||||||||  | ||||||||   |||||  || ||||||||  | ||  |||   
tatgtctaagtaagtt-gtggtatttttgt-cattttaatgtgctttgagggtaaatcatgaaatatatctttatg-tattattatattat-attatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttt---tcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
 |  ||   || ||||  | ||| |     | |    | |  ||||||   | | || || | | |||| |    || |||   | | |  |||||   ||||  || || |||||||| ||||||||||| || ||||||||||||||||||||||||||  | || |  || |||||||| || ||  |||   
attcagtccatgtttgttg-aatttatagaggtggtttttattttcag--ataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 4
-ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctg--atttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
     ||   || ||||  | ||| |     | |    | |  ||||||   | | || || | | |||| |    || |||   |  |  |||||   ||||  || || |||||||| ||||||||||| || ||||||||||||||||||||||||||  | || |  || |||||||| || ||  |||   
nnntcagtccatgtttgttg-aatttatagaggtggtttttattttcag--ataattgttcctcaaattcttctgtttatttgtgtacgctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG

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|218500747|gb|FG962718.1|FG962718
EST:     GCAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA                         GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
EST: gi|27576482|gb|CA999176.1|CA999176
EST:     AAGGGATGCTTCA                         GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: AAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
EST: gi|29616664|gb|CB621676.1|CB621676
EST:     GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA                         GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
                                      ctctgat  putative branch site (score: 4)
                              ttcttttcctctgatt  CT-rich tract
               ttaagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT