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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g32400.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 4
----------ctgttctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
           ||      || | || ||    | |    ||   | ||||   | | ||||   |  |  |||  |  ||||||||       ||||  || |||  ||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| |||
tttaaattttatggcaaaatattctctttgaaaaattacattgattaaagggtgagcatttgtact--gctggtc-tgctgctaatg-------atttcaaactgttcagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAATTCTGAAGGGTACAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
---ctgttctgctagtatcattcggtagtgtttttag---ctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
    | |  | ||     || | |  |      ||||    | ||      ||  ||  | || ||  |  |||| |||||    ||||  | |   |      |||||||||| ||||| || || ||||||||||||||||||||||| ||  | || || || ||||| |||
tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactg-gatat-gctaacatttttttttatcata----acagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G36130.3 (Glycine max), 3'ss of exon 7
ctgttctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
       |  |  ||  ||   || || |  ||  | ||  |     |||   ||      | ||    ||||||| |        |||||    |  |||| ||||| ||||| || ||||||||||| |||||||||||||||||||| || || || ||||  |||
-------gtaaacatatttaattaatgataata--ttaattagtgcacttcatttcgactggata----tgctaattg--------tttgataactacagACCTTTGTAGGAACACCATTTTGGATGGCTCCTGAGGTTATTCAAAACTCAGAAGGATATAATGTGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 8
ctgttctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaatt--ttgaattg-tgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
                    |  ||  | ||||  | || || ||    ||| ||   | |  | || |          |  |||||  ||||||   || |||| ||||| ||||| || |||||||||||||| |||||||||||||| || || || || ||||| |||
--------------------gtaagcatatttaatt-aatgataa--tattgattagtgcacttcatttcaactggatatgctaattgtttgaataactgcagACCTTTGTAGGAACACCGTTTTGGATGGCACCCGAGGTTATTCAAAATTCAGAAGGATATAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
ctgttctgctagtatcattcggtagt-gtttttagctcaaggacaaacctttgc--ttttggaaggtaatattgctaatggcttttaattttgaattgtg-tagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
   | ||  | ||   |||    | |   ||  || || |    |   || | |   | |  |   |    | | ||     ||||  ||||  ||  |   |||||||||| ||||| || || ||||||||||||||||||||||| ||  |||| || || ||||| |||
--atact--ttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 8
--ctgttctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtg-tagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
  |  ||     |  |||      |    || |  ||| | ||       ||| |  |            ||||   ||   |   || || ||   ||  |||| ||||| ||||| || |||||||||||||| || |||||||| ||||| || ||||| ||||| |||
atcaatttgaacaacatctcatctttac-ttctctgctgatggtttgcaattttcactcattcatctgggttgc--gtgcgctgatatgttaaagaatgacagACTTTTGTAGGAACCCCATTTTGGATGGCACCAGAAGTTATTCAGAACTCAGAAGGGTATAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------ctgt-tctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgt----gtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTG---ACGGGTACAATGAAAAG
                                                                       |||| |  |   | | |||  |   |  || |||  |       |||    || |||||      |||    | | |   ||  || | |||  |||    | ||||||||||||||||||| || |||||||| || ||||| || || |||||||   | || |||||||| |||
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------ctgttctgctagtatcat-tcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTG---ACGGGTACAATGAAAAG
                                                                                  ||      |   ||| | || ||  | | |  | ||||  |       ||||   |  ||| |    | |   | ||| |  |   | ||  ||    |||| |||||||||||||| || |||||||| || |||||||| || |||||||   | || ||| |||| |||
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttat-tctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatg--ttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG

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|33796053|gb|CF323894.1|CF323894
EST:     GTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: GTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|25799236|gb|CA755197.1|CA755197
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAATACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|58665909|gb|CK054595.1|CK054595
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|33796927|gb|CF324327.1|CF324327
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCC
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCC
EST: gi|58669013|gb|CK057699.1|CK057699
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
                                  ttttaattttgaattg  TA-rich tract