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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctccctacctcctatcttgcatttattatctgaagcttctcttcatacctagcaataccaaccggacgaacaacgtaaacatttgaaccgagtcacattttcgtgtcgtcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA

Basic information

species Oryza sativa
transcript LOC_Os02g06840.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 9
---------------------------------------gtaagctccctacctcctatcttgca----tttattatctgaagc-ttctcttcatacctagcaataccaaccggacg---aacaacgtaaaca--tttgaaccgagtcacattttc--gtgtcgtcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA
                                         |||||   |   || |   |  |           || ||||    |||  | | || | ||  |   |||| |  |   ||||| |  |||   |||  |  ||| | ||| ||     | | |  | |||||||||||| ||||| |||||||||||||||  |||||||||||| ||||||||||| |||||||||||||||||||| ||||| |||||||||||||| ||
gtgagttttttcatcacttcatgcccctgactgacaaactcaagcttgtttgttcatcattcacgaggccgcgccatttgaattgctcttctgaaacatggctttgggaacctgctgctgaacaatgccaactatttttcatggagcctcatcttatgacgcctttaaccacagATTGCGAATGGAAGGCTCAGGCGGGGAACGTCTGCGCCGCGTCGTTCGACTGGAGGTGCAGCGGCATATGCAACTCCGAGGGAAGGATCTGGGAGGTCCA

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 10
gtaagctccctacctcctatcttgcatttattatctgaagcttctcttcatacctagcaataccaaccggacgaacaacgtaaacatttgaaccgagtcacattttcgtgtcg---tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA
                     ||   |     |         |   ||  ||    | | || || | |  | ||  || |      || |||  |   |  ||    || |    |  | | ||||||| ||||||||||||||||| || |||| ||| |  || ||||| |||||||| |||||||| || ||||  ||    | ||||||| ||||||| ||
-------------------aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctg--ccaatgacattg----ttcaactaaaa-attttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA
















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|29682551|gb|CB678826.1|CB678826
EST:     AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTG                         ATTGCGAGTGGAAAGCTCAGGCGGGGACCACCTGCGCCGCGTCATTCGACT
genomic: AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTGgtaagctccc ... tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
EST: gi|86868611|gb|CI332988.1|CI332988
EST:     AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTG                         ATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
genomic: AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTGgtaagctccc ... tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
EST: gi|88274436|gb|CI394842.1|CI394842
EST:     AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTG                         ATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
genomic: AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTGgtaagctccc ... tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTG                         ATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
genomic: AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTGgtaagctccc ... tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACT
EST: gi|87006638|gb|CI295021.1|CI295021
EST:     AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTG                         ATTGCGAGTGGAAAGC
genomic: AGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGTACTCCGCCTGgtaagctccc ... tcgatcacagATTGCGAGTGGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacgaacaacgtaaacatttgaaccgagtcacattttcgtgtcgtcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA
            taaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctccctacctcctatcttgcatttattatctgaagcttctcttcatacctagcaataccaaccggacgaacaacgtaaacatttgaaccgagtcacattttcgtgtcgtcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT