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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT

Basic information

species Oryza sativa
transcript LOC_Os02g12800.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 4
gtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT
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gtaatttaaatgttgcaacaattg-gtttgtttagtcttttgtttgcatttatttgattgagcaccgaattc-tgtcatctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT

upper sequence: LOC_Os02g12800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 4
gtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT
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gtaattcaaatgtagcaaccattgggtttttt--agtctcctgtttgcatttatttttttagcactgaattc-tgtcatctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATTAT
















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|58652699|gb|CK041379.1|CK041379
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|58663459|gb|CK052145.1|CK052145
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|58663492|gb|CK052178.1|CK052178
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|14571342|gb|BI118710.1|BI118710
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|88991494|gb|CI034829.1|CI034829
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|58652610|gb|CK041290.1|CK041290
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|58599056|gb|CK009584.1|CK009584
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|33795619|gb|CF323679.1|CF323679
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|33797146|gb|CF324438.1|CF324438
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|58656426|gb|CK045106.1|CK045106
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGTGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
EST: gi|29678878|gb|CB675153.1|CB675153
EST:     AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATG                         TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT
genomic: AGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAAT

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: 61 (upstream exon), 53 (downstream exon)
Score: 52

GTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgata ... tttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttttctctctattgcttgatttagttctaagttcctctcattttcctgaagTTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT
                                   ttcctctcattttcct  CT-rich tract
                   ttgattta  TA-rich tract