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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcctattatcccagcccctgcattttactacttccatttttattaatgccagctcaacatgaaatttgagtttgtgcatataaaactcgcattgcatgaaactactgaattatataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 4
gtgatgcctattatcccagcccctgcattttactacttccatttttattaatgccagctcaacatgaaatttgagtttgtgcatataaaactcgcattgcatgaaactactgaattatataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG
                  |  |   || |  | |  |    | | |   |||||         || |  |||   ||||||         ||   |     ||| |  ||           | | |||| ||||| |||  ||||| |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| ||||||| |||
------------------gggcaaacaatgaagtgttcttttctcttaaaatgc---------ataacttttctctttgtg--------gcttttagcttgtgatatcacc----------attaatagctgtgctctttttcagACATGTGGGCGGTTGGTGCTATTTTGGCTGAGCTTTTTACACTGTCCCCACTTTTTCCTGGTGAAAG

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
gtgatgcctattatcccagcccctgcattttactacttccatttttattaatgccagctcaacatgaa--atttgagtttgtgcatataaa-actcgcattgcatgaaactactgaattat-ataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG
                                                |  |   ||||| |  |||   || | |  |||  ||| |  | | ||   | | ||   |   | ||    | ||  || ||  |||   |      |||| |||||||| |||||||||||  | ||||||||||||||  |||  ||| |||||||||||| |||
------------------------------------------------tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatc-atggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
















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|58694135|gb|CK082822.1|CK082822
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTG
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTG
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
EST: gi|86848584|gb|CI293908.1|CI293908
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTG                         ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC
genomic: TCGAGCTCCAGAGGTGCTGCTACAATCGTCAGCTTACACACCTGCTATTGgtgatgccta ... acttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgcattgcatgaaactactgaattatataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG
                              aactgat  putative branch site (score: 3)
                                            cacttcctc  putative PPT
                      aattatataactgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgcctattatcccagcccctgcattttactacttccatttttattaatgccagctcaacatgaaatttgagtttgtgcatataaaactcgcattgcatgaaactactgaattatataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG