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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatccatagtgcaatgcagattctgaagtgtacattctatgtagtgttgctgagagtttttcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA

Basic information

species Oryza sativa
transcript LOC_Os04g53760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
gttagtatccatagtgcaatgcagattctgaagtgtacattctatgtagtgttgctgagagtttt----------------tcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA------
|||||||||   |  || ||  || |||| || |||   || ||| |  ||||  ||  | |||                 | |  |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |  |||||   |||||   ||||||||| ||| ||||      
gttagtatct-caaagctatttagcttcttaactgt-tgttttattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGA---GTCTA---GTAAACAATGCACTATAAAGCATG

upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 12
----gttagtatccatagtgcaatgcagattctgaagtgtacattct-atgtagtgttgctgagagtttttcct--------atgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTC--TAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA
      |||  |  ||  | |  |     |     |   || ||| | |||| | | |      |  |||||||        ||   ||||  || |||||||||||||||||||| || ||||||||| |||||||  |   |  |||   |  |  |   |       ||  ||  | |||    |    
gtgaagtagagtatattcttcgttat---tcacagatcataaattttgatgttgaggtctaagaaaattttccttcttcaaaattaacagGTGTCTATGTTGGAAATATACAATGAAACCATTCGTGATCTGTTAGCTACAAATAAGTCATCAGCAGATGGAACACCAACACGTGTGGAAAATGGTACTC--

upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA12G34330.1 (Glycine max), 3'ss of exon 11
gttagtatccatagtgcaatgcagattctgaagtgtacattctatgt-----agtgttgctgagagttt-ttccta----tgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTC--TAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA
  |  |||  |   |    | |   || | |    |   | | ||||     | | ||   ||   ||  ||| ||    |   ||||  ||||||||||||||||||||||| || ||||||||| ||||| |  |   |  |||   |  |      |       || |||  | |||    |    
-gtgatatagagcatttccttctttttttcacacatgattgcaatgtttataaattttaaggatgattcgttcataaaatttaacagGTGTCAATGTTGGAAATATACAATGAAACCATTCGTGATCTGTTATCTACAAATAAGTCATCATCAGAAGGAACACCAACACGAGTGGAAAATGGTACTC--

upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------gttagtatccatagtgcaatgcagattctgaagtgtacattctatgtag---tgttgctgagagtttttcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATAC-ACCATAA
                             |||  | | |    | |  |    ||  | | || ||   ||  |||       |  || |   |      ||| || |||  ||||||||||||||||| ||||| |||||||||||||||||| || |   ||| ||      ||    |||  | | ||| |||   |    |   ||
gtgagcaagcaatattatcttgcctttttgttcattttctgcttaccctttgaatgtt-atgtctatggtcattgtgaacacatgtcttattctaagatatatttgtagGTTTCAATGTTGGAAATATATAATGAAACAATTCGTGATTTGTTATCAACAAATCGATCCTGCT-CTGATGTCTCACGAACAGAAAATGGTGTTGCTGGAA

upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 11
gttagtatccatagtgcaatgcagattct----gaagtgtacattcta---tgtagtgttgctgagagtttttcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA--
||  |  | |||  ||| ||  |  |||     |||| ||   ||  |     |    |   || ||    |  |    |||||||||||||||| ||||| ||||| || || |||||||||||| | ||    || |     |||     ||    |   |   |||     |  | ||| |  
gtacgattacatgctgccattaaccttcgtttagaagggtgggttggagaacattaactaattgcgaagcatggcaccttgcagGCATCAATGTTAGAAATCTACAACGAAACCATTCGTGATTTGCTGGCGAAAGGGCCAGTGAATGGAGATGTCAAGCAAAT--GTATGTGGTGAAGCATGACC

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|86829533|gb|CI286731.1|CI286731
EST:     TTAAGACAAGTCAGTCTCTTGAATCTCAAGGATGGAAGTACAGTATGCAG                         GCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCT
genomic: TTAAGACAAGTCAGTCTCTTGAATCTCAAGGATGGAAGTACAGTATGCAGgttagtatcc ... ctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattctgaagtgtacattctatgtagtgttgctgagagtttttcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA
                                       tttttcctat  CT-rich tract
                attctat  TA-rich tract