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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagtgctcatgcgctcatgcttagttttgcaagccaaaactggaatgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 2
--ttatagtgctcatgcgctcatgcttagttttgcaagccaaaactggaatgtagtttaactatatctgc-tgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
    ||  |  ||||  || ||   ||  |  ||||||   ||| ||  |  |  | |  |  | ||||| |  |||  | |  |   |||||   ||| ||||||| ||||| ||||||||||||||||||||||||| |||||| || |||  ||||||||||||||| |||||||||||||||||||||||| | |||||
gcagatgtttttcatctgcacacttttc-tactgcaagtttaaa-tgacagatgatgtt-cagtctctgcattctctcaactcatttgactatccttttacagTTGACCCTGAAGATATTCCATTGGAGAAGGTTCAAGTTAAATCCTCAGGACATGTTCTGCCATATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 2
----ttatagtgctcatgcgctcatg-cttagttttgcaagccaaaactgga-atgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
      ||| || ||||| || | |  |||  |  | |||    |||  | | |||  |||||    |  ||||||||||   |  ||   ||||  | | | ||||||| ||||| ||||||||| ||||||||||||||| |||||| || |||  |||| |||||||||| || ||||||||||||||||||||| | |||||
ttgcagataatgttcatgtgcacttaactttctactacaaatttaaatggcagatggtgtttag---tccctgctgatctc--tcgctttgactacct-tatacagTTGACCCTGAAGATATTCCACTGGAGAAGGTTCAAGTTAAATCCTCAGGACATGTTATGCCATATGTTGGTGTTGCTTGTTTGGGGGCTATTCTGTTTGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 2
ttatagtgctcatgcgctcatgcttagttttgcaagccaa--aactggaatgta-gtttaactatatctgctgatcttgatttctaatactatttatttccagTTG---ATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
   | |    | |    |     |    | ||  | |     | |||  |  ||   ||   | |   | | |||  | ||    | ||  ||| | || ||| ||   |   ||| ||| ||      |  |    ||| |  ||||||||||||| |||||| |||||||| || ||||||||  | || || ||||||||   
---ttggaaacttagatttgaattgcaatatgataactttctagctgttacatatacttgtatgttcttacagatactcatagaaagtaaaattgagttgcagATGGAAACATTGAAGATGTTGTTCCAGCTACTCCTCAGGGCAAATCTTCTGGAAATGTTCTACCATATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATT---

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|88740945|gb|CI763460.1|CI763460
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTA
EST: gi|88738909|gb|CI762417.1|CI762417
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88385512|gb|CI564172.1|CI564172
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88745094|gb|CI768454.1|CI768454
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAA
EST: gi|86849748|gb|CI301637.1|CI301637
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88368202|gb|CI575084.1|CI575084
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88745134|gb|CI768494.1|CI768494
EST:     GGCCCGCGCTCGAGCCCGCGCTACTCCCGCGGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: GGCCCGCGCTCGAGCCCGCGCTACTCCCGCG-TGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|86832143|gb|CI305369.1|CI305369
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88732120|gb|CI757297.1|CI757297
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCCCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|300215629|gb|HO088255.1|HO088255
EST:     CGCGCTACT-CCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCCTTGTTAGAAGGTTCAAGCTAAATCTTCTGGA
genomic: CGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTG-GAGAAGGTTCAAGCTAAATCTTCTGGA
EST: gi|88740564|gb|CI764072.1|CI764072
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
                                 ttctaat  putative branch site (score: 2)
                                            tttatttcc  putative PPT
                            ttgatttctaatacta  TA-rich tract