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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatattgattatcttaactagtgtaatgtgcttgagtattttcttcaagttatgtccttatgctagatactgtactcaaccctactcttctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATCAACAACAGGCAATATCGAG

Basic information

species Oryza sativa
transcript LOC_Os03g21720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G067546_T01 (Zea mays), 3'ss of exon 3
--------gtatgtaatattgattatcttaactagtgtaatgtgcttga-gtattttcttcaagttatgtccttatgctagatactgtactcaaccctactcttctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATCAACAACAGGCAATATCGAG
        | | | | ||    |  | || || | ||  |  ||||| |  ||||||| ||||  | ||    ||| ||   | ||          || || || |  ||||||||||||||| |||| | ||||||||||||||||| |||||||||||||||||||||| ||||||| |||
tttcaaatggagggagtaacattgttgtttacaaatgctacttgctttacatattttcatcaatctgtgg---tatacttagttct----------ctgcttttattatatagATTGGTCATGGTAAAAGGGGAGATGTCACAATACTACCAACCCTTGTCATCAACAACAAGCAATATAGAG

upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G049211_T01 (Zea mays), 3'ss of exon 4
gtatgtaatattgattatcttaactagtgtaatgtgcttgagtattttcttca-agttatgtccttat-gctagatactgtactcaaccctactcttctatt--atagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATCAACAACAGGCAATATCGAG
          | |   | || |  |  || | | |  | | | ||     |   |||   ||  || | | |  |   | | || |   ||   ||| || |  |||||||||||||| |||| | ||||||||||||||||| |||||||||||||||||||||||||||||  |||
-------gcttaggacaact-agatcttgaagttttttgggggatgcaggtggtagtagagtaattgttggtcaaaggtatccttagttctttgcttttactgtatagATTGGTCATGGTAAAAGGGGAGATGTCACAATACTACCAACCCTTGTCATCAACAACAGGCAATACAGAG
















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|88259865|gb|CI364356.1|CI364356
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
EST: gi|29665176|gb|CB661451.1|CB661451
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
EST: gi|29684200|gb|CB680475.1|CB680475
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
EST: gi|58692052|gb|CK080739.1|CK080739
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
EST: gi|88377023|gb|CI597807.1|CI597807
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAAGGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
EST: gi|55411780|gb|CV724156.1|CV724156
EST:     CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAA                         ATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC
genomic: CTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 70 (downstream exon)
Score: 88

GGTTGGATGTTGAGAAGATAAAGAAGTGTGTTGGAGATCCTGAAGCTGATGAGGAAAACCCTGTTCTGAAGGCAGAACAAGATGCCCAAgtatgtaata ... tctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATCAACAACAGGCAATATCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagttatgtccttatgctagatactgtactcaaccctactcttctattatagATTGGTCATGATAAACGAGGAGATGTCACAATACTGCCAACCCTTGTCATCAACAACAGGCAATATCGAG
                                    ccctactcttctatt  CT-rich tract
                                            ttctattata  TA-rich tract