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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG

Basic information

species Oryza sativa
transcript LOC_Os03g38590.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcatttt--ttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
                ||  ||  | | |||| |   |    |   |  ||  |||    || | |  | |    ||| | || ||    ||| ||     |     |||   |   | ||         | ||||||| ||||| ||||| |||||||||||||||||||| |||||||||
---------------gtaaatgcaatagattaaatcgtttcctccctatgaatattacagttattatatctctacttggtgagctccccgtaaaattattatccactataccgtgcatgtgt--------ttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG

upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataa-tttatttctgcaaaacgtat-cacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
                                          |   || ||| ||        | ||  | |  |   ||     || ||| || ||  |  |  |||| ||| | ||||||| || | |   |||||| ||||| ||||| || || |||||||||||||| |||||||||
-----------------------------------------gtaaatgcgatgatacccac--aagtcgtttcctcccta----caaataacatttcactctcatataagtttctgtctgcaacacatgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG

upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatca-cagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
                            |||  |    |||||  |  | |  ||        | |  | |   | || |  |     | || |  ||||       |  ||   | |||    | | |   ||||||||| |||||| ||||||||||||||||||||||||| ||  ||
----------------------------attgaa----gcattcatgagaacaataggcaaatatgcatgcatattttcatctt---tttattttgccttactgttgatcttgaatatgctgctctttttttcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCCTGTTTTATCTG

upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 7
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattt--tttgtgaggttttctgttgtttagttcgaactaatatctc--cttggctcataat-ttatttctgcaaaacgtatc-acagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
                                        |  | | |   ||| ||  | | | |  |||  | ||| | ||    ||  || |  |     |  ||  | || ||   | |||    | | |   ||||||||| |||||| |||||||||||||||||||| |||| ||  ||
----------------------------------------acctctggtactcaattaatatataatatttatttttgctgagcaaaaaaaaaaaatttggtcttactgttgatcttgaatatgctgttcttttttgcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCATGTTTTATCTG

upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
                               |  ||    || | |  |  |   | | |||  |  | | |||| | | |||  | || | |  |   ||     | ||      || ||| |  | | |||||||||| |||||| |||| ||||||||||||||| |||| || |||
-----------------------------ccaccatccatatgtgt--gtgtgcatgtatgtttgtatgtgtgtt-tatggttttacctgacaattttctgttatctgatca--cactacaacatttcttacagGAATGAAAGTGCTTTGAAGTTTGGATGGTTTTTCATGTTTTATTTG

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|25799630|gb|CA755591.1|CA755591
EST:     TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG                         GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG                         GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG                         GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
      aactaat  putative branch site (score: 2)
                        tcataatttatttct  TA-rich tract