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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaattgatgcccttcaacctttacactcaatgagtcaatgtctagtttgtcaagatacagctactttaatgcttaacaatttttcagtttgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAAGCAAGGATGAGGAATCAAGTAATGCTTTGCTAATGAGGGCCTGGTCTCC

Basic information

species Oryza sativa
transcript LOC_Os02g41550.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G172152_T01 (Zea mays), 3'ss of exon 3
---gtaattgatgcccttcaacc-tttacactcaatgagtcaatgtctagtttgtcaagatacagctactttaatgcttaacaatttttcagtttgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAAGCAAGGATGAGGAATCAAGTAATGCTTTGCTAATGAGGGCCTGGTCTCC
    || |   |||   || ||  |||  | | ||||  ||       | |   |||  |||   || ||||||   |    ||| |||  || | | |||||||| | |  | ||||||  | |||||  ||||||| ||||| |||||||| || ||||||| ||||||||| |||||||||||||  ||||||||||||||
gtcttagtgattgcttctctactatttggatttaatgcttctccaatcaataaatcatcatatttctgctttaacttt----aatattttggtataaaattcagGTCTAGCAAATGTTCGCTGTTGTTCGATTGATGATCTAGGTCTTGAATCTAGTAAGGATGTGGAATCAAGCAATGCTTTGCTAAGCAGGGCCTGGTCTCC
















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|29674937|gb|CB671212.1|CB671212
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29629647|gb|CB634656.1|CB634656
EST:     TATTGACGTATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTANGACTTGAAT
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAAT
EST: gi|29671259|gb|CB667534.1|CB667534
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29627388|gb|CB632399.1|CB632399
EST:     TATTGACGTATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29641884|gb|CB646891.1|CB646891
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29668745|gb|CB665020.1|CB665020
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtcaagatacagctactttaatgcttaacaatttttcagtttgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAAGCAAGGATGAGGAATCAAGTAATGCTTTGCTAATGAGGGCCTGGTCTCC
                            ttaacaatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatgcccttcaacctttacactcaatgagtcaatgtctagtttgtcaagatacagctactttaatgcttaacaatttttcagtttgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAAGCAAGGATGAGGAATCAAGTAATGCTTTGCTAATGAGGGCCTGGTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG