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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG

Basic information

species Oryza sativa
transcript LOC_Os03g15780.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 7
-gtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG
 |      ||      |   ||   | ||   ||| ||||    || |  |       |   |  ||| ||      |||||| |||| | |      ||||  |||| |||||||| ||||| |||||||||||||| || |||||||||||  | ||||||||||| ||||||||||| || |||
agccatcctttaaaagtcatgaaaacgga--tatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatgactgcg----gcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctact-tggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG
  || | |   | | | |  ||   | | |  ||  |  |||  |||  ||||    |  |     ||   | || |||| |  | | ||||  ||  | |  ||||| ||||||||||| |||||||  || || ||  | ||||| ||||| |||||||||||||||||||||||||| ||||||
--ttatatgtctatatatatatatataaat--tgtctaaatttctttttcagagc-atatgcttaatggccataa-ttttgtagttaatactagctgttcttacagGTGTCCAAACCTGGTTCTGTGACTGTTGAAAAGCTCATGAATATTGAGCGCTACTCCCATGTCATGCACATCAGCTCCACG
















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|29616044|gb|CB621056.1|CB621056
EST:     TGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTT-GANAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACG
genomic: TGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGA-AAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACG
EST: gi|29662736|gb|CB659011.1|CB659011
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGGATGATG-TGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29646546|gb|CB651553.1|CB651553
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29662735|gb|CB659010.1|CB659010
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29628879|gb|CB633890.1|CB633890
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29614551|gb|CB619564.1|CB619564
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG
                tgttaac  putative branch site (score: 2)
                                        ctttctactt  putative PPT
                          ttttcttatgatta  TA-rich tract