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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggaatctttttcccccacgaagaaattcagcaatttggtttcacggagcatagagcttgggaattctgcaaaaaaaaaaaaagaaaaaaagttaatgagatttgacgcgctaacgctaaatttggtgaaatgttgtgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG

Basic information

species Oryza sativa
transcript LOC_Os04g45190.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155543_T01 (Zea mays), 3'ss of exon 2
gtaactggaatctttttcccccacgaagaaattcagcaatttggtttcacggagcatag---agcttgggaattctgcaaaaaaaaaaaaagaaaaaaagttaatgagatttgacgcgctaacgctaaatttggtgaaatgttgtgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG
                            ||  || ||| | ||  | | |        |   |||| |     | ||  ||    | | |||  |  || |   ||| |       || | | | ||   ||  ||  || ||| |  |   |||| ||||| || ||||| ||||||||||| ||| |||| ||||| ||||| ||||| || |||||||||||||||||||| |
--------------------------gtaagctcggcattctgaatcccctctttcccgcccagctagattgctttgtcaaggtcatagaagtcagcaactgcgtgaaa-------cgttga-gttactattaatg--attttgagtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTG
















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|163928274|gb|EG714654.1|EG714654
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGTCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|428790|gb|D24946.1|D24946
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGNCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|88851478|gb|CI670918.1|CI670918
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|88317555|gb|CI672132.1|CI672132
EST:     ATGCCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: ATGC-TCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|88330878|gb|CI636890.1|CI636890
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|117238779|gb|CT842528.1|CT842528
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|163929272|gb|EG712701.1|EG712701
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTG
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTG
EST: gi|58606663|gb|CK034696.1|CK034696
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
EST: gi|163929427|gb|EG713396.1|EG713396
EST:     CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG                         GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT
genomic: CATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATT

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: 72 (upstream exon), 58 (downstream exon)
Score: 21

TCGAGACGAAGAAGCAGATCTCATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaactggaa ... tgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatgagatttgacgcgctaacgctaaatttggtgaaatgttgtgctccttagGTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG
                                             tgctcctt  CT-rich tract
                          taaattt  TA-rich tract