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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccctctcatactttagggtaaaattttttcctgaatttgcatgctattttctttgattttgtggacagatatatcatatattaattactgtattctcaccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT

Basic information

species Oryza sativa
transcript LOC_Os10g32730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 5
gtaaccctctcatactttagggtaaaattttttcctgaatttgcatgctattttctttgattttgtggacagatatatcatatattaattactgtattctcaccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT
            ||  |  |   ||||||     |||| |   || | | ||||  ||   ||  ||      |   | |  ||||| | | | | || | | | ||| |||| ||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||  ||||
-----------gtatctctg---aaaatt-----ctgattagacacgatctttttctt---ttcatgt-----tgagttacttattagtgaatttgttattatcttgtatagGGTGGAAAGAGTCTTTCTCTGCAATTGTTGGTGGAGATGAAGTAGAGAAGGGGAAGCCATCCCCGAATAT
















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|157651850|gb|EX451484.1|EX451484
EST:     AGATC-AACATTGACGC-AAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: AGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29631920|gb|CB636929.1|CB636929
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGA
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGA
EST: gi|29687643|gb|CB683918.1|CB683918
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29636237|gb|CB641246.1|CB641246
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAA                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATG
EST: gi|29671819|gb|CB668094.1|CB668094
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29658982|gb|CB655257.1|CB655257
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29629324|gb|CB634335.1|CB634335
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|58688816|gb|CK077503.1|CK077503
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29679504|gb|CB675779.1|CB675779
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29623338|gb|CB628349.1|CB628349
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
EST: gi|29659012|gb|CB655287.1|CB655287
EST:     TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAG                         GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG
genomic: TTCCAACTCACCAAGATCAAACATTGACGCAAAAATTTCCTGCCATCAAGgtaaccctct ... ccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttgtggacagatatatcatatattaattactgtattctcaccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT
                                       ttctcac  putative branch site (score: 2)
                                       ttctcacc  CT-rich tract
             agatatatcatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccctctcatactttagggtaaaattttttcctgaatttgcatgctattttctttgattttgtggacagatatatcatatattaattactgtattctcaccatgtttagGATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG