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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g45350.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 5
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG----------------------
        || ||    || |||| || |  | ||  ||| ||| ||| |  |  |||  ||  |||  ||| ||   | |||||||| ||||| ||| |||||||||||||||||||||||||||| |||||||| ||||||||||||                      
-------gtttgtc-taatcgcatcttcaacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020574_T08 (Zea mays), 3'ss of exon 5
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
        || ||    || |||| || |  | ||  ||| ||| ||| |  |  |||  ||  |||  ||| ||   | |||||||| ||||| ||| |||||||||||||||||||||||||||| |||||||| ||||||||||||
-------gtttgtc-taatcgcatcttcaacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020574_T03 (Zea mays), 3'ss of exon 5
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG----------------------------------
        || ||    || |||| || |  | ||  ||| ||| ||| |  |  |||  ||  |||  ||| ||   | |||||||| ||||| ||| |||||||||||||||||||||||||||| |||||||| ||||||||||||                                  
-------gtttgtc-taatcgcatcttcaacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTGGTATGTGCTGTG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 5
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
        || ||    ||  |||||| |  | ||  ||| ||  ||| |  |   ||  || ||||| ||| ||   | |||||||| ||||| ||  |||||||||||||||||||||||||||  |||||||| ||||||||||||
-------gtttgtc-taatcacattttcaacagtgccaatactcatagaaacacagttagtgattaagcaattatctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 5
-------------------gttagtacttagtaacgattgcatttttattaatgtaaatgcttg-tagtagtatta-----ttcatgtt-taa------------gaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
                      | | |||  || |  |    |   |   ||  |||| ||    ||| || ||||      | || || |||            || |  ||||||  ||||||||||||||||||||| |||| |||| ||||||  ||||||||| ||||||||||||||||||
gtgcgagtgttcgcatccatccaatcctttcta-ctctcctctccctgcaaaaataaaagcaaaatagaagcattaagctgcttattttgtaaactggcataattgagaccatgctttcagATGCTTGGAGTCAAGAGAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G16860.2 (Glycine max), 3'ss of exon 5
----------------------------gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtag--tattattcatgtt----taa--gaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
                              |  | |    |  |      | |   |  ||  || | || |  ||  |  |||| |  |   |    |||  || |  ||| ||  ||||||||||||||||||||| |||| |||| ||||||  ||||||||| ||||||||||||||||||
gtgcgagtgttcgcatccatccaatccttctgctcccctctccctgcaaaaataaaagaaaaatagaagcattaagctgcttattttgtaaactgacataattgagaccatgttttcagATGCTTGGAGTCAAGAGAATTGAACGGGTACTTCCAGTTGGAACTTCCTTGACTGTTGTTGGTGAG

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 5
gttagtacttagtaacgattgcatttttatt-----aatgtaaatgcttgta-----gtagtattatt-catgtttaa------gaaataatgcttgta-gATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
||| || ||    |  | |||||  || | |      |   | |   ||| |     ||    || || || | ||||      | ||| ||| || || |||||| ||||| ||| ||| |||  |||||||||||||||| ||  | ||||||||||||||||||
gtttgtcctattcagtgtttgcaaattaacttaaaagacacacacctttgcatgcatgtgccgttgtttcaagcttaatttttggcaattatgtttttaagATGCTCGGAGTGAAGCGAATTGAGCGGGTTCTTCCAACTGGCACACCTTTGACTGTTGTTGGTGAG

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|58695660|gb|CK084347.1|CK084347
EST:     CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAG                         ATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAA
genomic: CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAGgttagtactt ... atgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAA
EST: gi|29684518|gb|CB680793.1|CB680793
EST:     CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAG                         ATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTG
genomic: CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAGgttagtactt ... atgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTG
EST: gi|58693123|gb|CK081810.1|CK081810
EST:     CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAG                         ATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCA
genomic: CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAGgttagtactt ... atgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCA
EST: gi|29680615|gb|CB676890.1|CB676890
EST:     CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAG                         ATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTG
genomic: CAGGGCGGACACTTGTGCGTGGAACTCTAGACTATTTACAAGGGCTGAAGgttagtactt ... atgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
 tattaat  putative branch site (score: 2)
                    tagtattattcatgtt  TA-rich tract