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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagattaaccttttttttgtgttaactagattcactataattttgtgagtgcaccatgtgctattcagcattatatatttattccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g47350.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G415846_T01 (Zea mays), 3'ss of exon 9
gttaagattaaccttttttttgtgttaactagattcactataattttgtgagtgcaccatgtgctattcagcattatatatttattccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaattt-gcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAA---
||||||  | | | |||| |  | | || |||| |||| ||  ||     ||| | | | ||  ||||                |||  | ||| ||||| ||   ||  |    |||  | | |  | | | ||| ||||||||||||||||||||| || || ||| ||||||| ||   ||||  ||  || |||   || ||  ||||||| |||||| | |||||  |  |        
gttaaggattaaccttttctcctctaaagtagactcacaatgttt-----agtac-ctaagttgtatt----------------ttcagttgctttctgcctcaccctcttggattgacacatttattttgacttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGAT---TGGCGATGGCTTTGCTAATTTTCTTACTGATATTTTTATTGACAAGGACAAAAACGAGGATG

upper sequence: LOC_Os06g47350.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G34750.1 (Arabidopsis thaliana), 3'ss of exon 10
gttaagattaaccttttttttgtgttaactagattcactataattttgtgagtgcaccatgtgctattcagcattatatatttattccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAA
             |  |   | |    |  | |||    |||||| |||   |    | | |    |  |||||  |  |  |      ||       | ||  | ||   | |||   ||           || |||||||| | || || |||||||||||||||||||||||||  |||||  |  |||| |||      ||    || || ||| |    |   |  || ||  | 
------------gtagtccatatagctatcatattttgcataattatgtacatat-tcttctagactctagcatggtcgacatgaaatgtc-----tcggtttatactcactttctatatc-----------atctgcagTTTCTGATATTCTATGCCTGCTCACTGGATCCTGAAAATTGTGGTGTGAAATTTGCTAGTAAGCTAGTGGAGATTTTTCTCTCCAGCAACAAGCATGTAG
















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|29681086|gb|CB677361.1|CB677361
EST:     CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAA
genomic: CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAGgttaagatta ... aaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAA
EST: gi|29628119|gb|CB633130.1|CB633130
EST:     CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGTCTTGAA
genomic: CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAGgttaagatta ... aaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAA
EST: gi|29689750|gb|CB686025.1|CB686025
EST:     CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAA
genomic: CTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAGgttaagatta ... aaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAA
                           atctgat  putative branch site (score: 4)
                                          tgtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagattaaccttttttttgtgttaactagattcactataattttgtgagtgcaccatgtgctattcagcattatatatttattccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaatttgcagTTTATCATGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT