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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatgtcatctgaatccatttccccttcagatatatcacatgtactctcttcctaaatagacttggttctggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g36270.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 4
gtaaccatgtcat-ctgaatccattt------------ccccttcagatatatcacatgtactctcttcctaa----atagact--tggttctgg-tatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG
||||| || |  | ||  ||||| ||            |||   | |  |  |||| |  ||||   |  |||    || ||||   | | |    |||| ||||||||| |||||||||| || ||||| || || ||||| || |||||||||||||| ||||||||| ||||||||||||| ||||||
gtaactatctattgctagatccactttagtttttacgccccggccggccaattcacttcgactcgtcttataactgtatcgactgccgttaccaactatggcagCTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAG

upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 7
-gtaaccatgtcatctga---atccatttccccttcagat-atatcacatgtactct-cttcctaaatagacttggttctggtatg----------acagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG
  ||||  | |   |||    |||||    |  || |  | || | | |  |||  | |||  | | | || |    | |||||||           ||||||||||| |||||||||   || || || |||||||||||||| || || ||||| |||||||| || ||||| || ||||| |||
aataacattttttcctggtatatccaaggactgttgacttcattttaaacttacaatgcttaattactggattacaatttggtatgtaatggatttgcagCTTGTGTTAAGCACTGGAGCAGGTGTTAATGGTTTCACCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG

upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtaaccatgtcatctgaatccatttccccttcaga-tatatcacatgtac-tctcttcctaaatagacttggttctggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG
                  | | | |  ||||      | |    ||   | |  ||    | ||  | |   | ||| |   | |    ||  | || ||||||||||| |||||||||| ||| || || || || ||||||||||| || |||||||||||||| || ||||| |||||||| |||
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttg-cagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG

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|29670800|gb|CB667075.1|CB667075
EST:     GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACG                         CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
genomic: GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACGgtaaccatgt ... ggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
EST: gi|33684972|gb|CF313211.1|CF313211
EST:     GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACG                         CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
genomic: GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACGgtaaccatgt ... ggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACG                         CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCCTTC
genomic: GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACGgtaaccatgt ... ggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCC-TTC
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACG                         CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
genomic: GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACGgtaaccatgt ... ggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
EST: gi|29663073|gb|CB659348.1|CB659348
EST:     GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACG                         CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC
genomic: GAACAGACATGCTTGCTGCTGGCTACTGCATGTACGGGAGTTCATGCACGgtaaccatgt ... ggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagatatatcacatgtactctcttcctaaatagacttggttctggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG
                         tcctaaa  putative branch site (score: 2)
     atatatca  TA-rich tract