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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcattctattaactttatttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC

Basic information

species Oryza sativa
transcript LOC_Os10g38980.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
gttagt-tcattctattaactttatttggtt---tccatcgg--tctgaagtcctgtgctaatg-ccaaccttcctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
|| ||  |||    || |||||| | | |||   |||||     ||   ||     |||||||  |||| ||||  | ||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||
gtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC

upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G162251_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------gttagt-tcattctattaactttatttggtt---tccatcgg--tctgaagtcctgtgctaatg-ccaaccttcctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
                                                                                                                  || ||  |||    || |||||| | | |||   |||||     ||   ||     |||||||  |||| ||||  | ||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||
gtatgcactgaagcactatttacttatcttaatattttattcatcatgcaacccctttattaactcttcttttctcctggcaccatgtaaatgaagcagattttggacagcaaggtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC

upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
-----------------------gttagttcattctattaactttatttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctt--tttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
                       || | | ||| ||  | | | |  |   ||   |  |   ||  |     || | |  |     ||  ||  | |||||||||| ||||||| ||||| |||  |||  |  ||||||||||| |  | ||| |||| |||||||||||||||||||| |||||||| ||||| |||||
gaaaaagctccttttaaagcacagtaaatacatgct--tgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC

upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
-----------------------gttagttcattctattaactttatttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctt--tttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
                       || | | ||| ||  | | | |  |   ||   || |   ||  |     || | |  |     ||  ||  | |||||||||| ||||||| ||||| |||   ||  |  ||||||||||| |  | ||| |||| |||||||||||||||||||| |||||||| || || |||||
gaaagagctccttttaaagcacagtaaatacatgct--tgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC

upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G30700.1 (Arabidopsis thaliana), 3'ss of exon 5
------gttagttcattctat----taactttatttggtttccatcggtctgaagtcc---tgtgctaa----tgccaaccttcctttttg----------------tagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
       | | |||||   ||     ||  || |||| | |   | | | |   | |    |  | |||    ||  ||   || ||||||                |||| ||||| ||  | ||||  ||| ||||| |  ||||||| ||  |  | |||   || ||||||||||||||||  ||||||||||| || ||||||||
gtttgcatcaattcatctcatattccaaagttgtttgatatgtgttgttgtctcgccagaataagttaaaaagtgttaatgatcttttttgggtaacaatgtgattatagGTTGTCTTCTGAGAAGCTATCCTGCAGACTTGATATTTGATAACACATCAGGCTACAGCTTTACATGTGATTTGACAGACAACATTGCTGCTCCATGGCC

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|27547665|gb|CA765589.2|CA765589
EST:     AGCCTGCAAGCATTTGGTCAGCAAG                         GCTGTCCACTTCGCAGCTTACCTACAGACATTGGTATTTGACAATGCTACG
genomic: AGCCTGCAAGCATTTGGTCAGCAAGgttagttcat ... ctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTG-TATTTGACAATGCTACG
EST: gi|27920414|gb|CB096222.1|CB096222
EST:     AGCCTGCAAGCATTTGGTCAGCAAG                         GCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGG
genomic: AGCCTGCAAGCATTTGGTCAGCAAGgttagttcat ... ctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGG
EST: gi|58602511|gb|CK013039.1|CK013039
EST:     AGCCTGCAAGCATTTGGTCAGCAAG                         GCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGG
genomic: AGCCTGCAAGCATTTGGTCAGCAAGgttagttcat ... ctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
                            tgctaat  putative branch site (score: 2)
                                    ccaaccttccttttt  CT-rich tract
                                              tttttgta  TA-rich tract