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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctacttgatactgttaaaccggtgtgcttttacctttgaccggtataaaaacttccaaattagatgtcaattagattatcaaatatacttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGGGCGGCGCGGTTGCGCTGCTGCTGCACCGCAAGGACCCAACCTTCTGGGA

Basic information

species Oryza sativa
transcript LOC_Os05g29974.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29974.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G306851_T02 (Zea mays), 3'ss of exon 4
cttctacttgatactgttaaaccggtgtgcttttacctttgaccggtataaaaacttccaaattagatgtcaattagattatcaaatatactttttt-cagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGGGCGGCGCGGTTGCGCTGCTGCTGCACCGCAAGGACCCAACCTTCTGGGA
           |||   |||||   | | | ||     ||    |||| ||    | |||           | ||  ||  |    |  ||| || | ||||  ||||||  |||||  ||||||||||||| || ||||| ||||| |||||||| || || || || ||||||||| | ||||| || |||||||||||
----------gtacg--taaacatcttttccttggaaattactgggtaaaagtgttaccaggacctgaaaaagttt-atagtagtttgaactcttctgcagACATGGAGGGATACAGGAACAAGAGCCGGTTTCTATACGGCGAGTCCATGGGCGGAGCCGTGGCTCTACTGCTGCACAGGAAGGATCCGACCTTCTGGGA
















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|88356078|gb|CI627526.1|CI627526
EST:     GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTG                         AGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
genomic: GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
EST: gi|88416988|gb|CI573703.1|CI573703
EST:     GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTG                         AGCTGGAGGAGTA--GAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
genomic: GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
EST: gi|58609664|gb|CK037697.1|CK037697
EST:     CTTCAAATC-ATATGTG                         AGCTGGGGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
genomic: CTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
EST: gi|88760430|gb|CI769986.1|CI769986
EST:     GTTCGAGCATCTTGTCGATAACTGCGACAGATTCTTCAAATCAATATGTG                         AGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACG
genomic: GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACG
EST: gi|29656345|gb|CB652620.1|CB652620
EST:     GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTG                         AGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
genomic: GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
EST: gi|88743266|gb|CI766774.1|CI766774
EST:     GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTG                         AGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG
genomic: GTTCGAGCATCTTGTCGATGACTGCGACAGATTCTTCAAATCAATATGTGgtaaagaaaa ... cttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataaaaacttccaaattagatgtcaattagattatcaaatatacttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGGGCGGCGCGGTTGCGCTGCTGCTGCACCGCAAGGACCCAACCTTCTGGGA
                                           tacttttttc  CT-rich tract
                        tcaattagattatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctacttgatactgttaaaccggtgtgcttttacctttgaccggtataaaaacttccaaattagatgtcaattagattatcaaatatacttttttcagAGCTGGAGGAGTACAGAGACAAGAGCCGGTTCCTGTACGGGGAGTCGATGGGCGGCGCGGTTGCGCTGCTGCTGCACCGCAAGGACCCAACCTTCTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC