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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttttcactggtttatagtcgttatgaatcactaaaatctgaagaaattgtttgtggtccttaccaatggcactgccatttgggattttgggggtgaaatgttggccttctgcttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGAGCTTCGATCTCGTGATTGAGAAAGGCACCATG

Basic information

species Oryza sativa
transcript LOC_Os11g35340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G109032_T02 (Zea mays), 3'ss of exon 3
gtaaatttttcactggtttatagtcgttatgaatcactaaaatctgaagaaattgtttgtggtccttaccaatggcactgccatttgggattttgggggtgaaatgttggccttctgcttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGAGCTTCGATCTCGTGATTGAGAAAGGCACCATG
                                                          ||  |  || |  |  |        ||||     |  ||| ||| || ||||   | |||| |||||||| ||||| | |||||| ||||||||||||||||||||||| || | ||||||||| |||||||| ||||| || |||||||||
----------------------------------------------------------gtaatt-ttgctgacagaggaagtttttgcaccatccgggttgagattttggttct-tgctccttgcagGCGTGGATGCTGTGGTTGCGGACATGCTTGATCTGCCGTTTGAGCATGAGAGCTTTGATCTCGTCATTGAAAAGGGCACCATG
















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|88373272|gb|CI614608.1|CI614608
EST:     CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGG                         GTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGACA
genomic: CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGGgtaaattttt ... cttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGA
EST: gi|58654845|gb|CK043525.1|CK043525
EST:     CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGG                         GTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGA
genomic: CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGGgtaaattttt ... cttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGA
EST: gi|58587157|gb|CF985465.1|CF985465
EST:     GGGCACCGAGG                         GTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGAGCGGGAGA
genomic: GGGCACCGAGGgtaaattttt ... cttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGA
EST: gi|88392707|gb|CI623938.1|CI623938
EST:     CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGG                         GTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGAT
genomic: CGTCGCCGTCCAGCGGATGCGTGACCGCCTCGCGGAGCAGGGCACCGAGGgtaaattttt ... cttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcactgccatttgggattttgggggtgaaatgttggccttctgcttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGAGCTTCGATCTCGTGATTGAGAAAGGCACCATG
                                      ccttctgcttcttgc  CT-rich tract
                             aaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttttcactggtttatagtcgttatgaatcactaaaatctgaagaaattgtttgtggtccttaccaatggcactgccatttgggattttgggggtgaaatgttggccttctgcttcttgcagGTGTGGAGGTTGTGGTGGCGGACATGCTTGATCTGCCGTTCGATCGTGAGAGCTTCGATCTCGTGATTGAGAAAGGCACCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT