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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattgagccttcattgtcatccctatttatttactctattcagtaaaacatcctgttctgtggatctgtagaatgatgtatctcttatagaaatt...

Basic information

species Oryza sativa
transcript LOC_Os03g55389.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 3
TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattgagccttcattgtcatccctatttatttactctattcagtaaaacatcctgttctgtggatctg---tagaatgatgtatctcttatagaaatt
 || ||||| |||||||  |||||||| ||||||||||||||  |||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||| | |||| || | ||   |  |    |  |  | | | ||| || || |  ||  | |  ||||||  |    |    |  | | | ||||||     | 
CAGTTTGATATTTGAATTCGTCAACAACACAGACTTCAAAGTTTTGTACCCCACATTGACGGATTATGACATCCGCTACTACATATATGAGCTACTCAAGgtcatgattg-gcatccaaattatttgacacgttgtcatt-tatacattacattatttt-tcttgtggaaatagtttcaggtagtttctttcttatttggtta

upper sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 3
TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattga-gccttcattgtcatccctat-ttatttactctattcagtaaaacatcctgttct-gtggatc--tgtagaatgatgtatctcttatagaaatt
 || ||||| |||||||  |||||||| ||||||||||||||  |||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||   ||||    ||  ||| |    |  || | ||||||||  ||    |  ||||  | || | ||||||   | |  | |  |   | ||||||       
CAGTTTGATATTTGAATTCGTCAACAACACAGACTTCAAAGTCTTGTACCCCACATTGACGGATTATGACATCCGCTACTACATATATGAGCTACTCAAGgtcacgattgccatctgaattatttgacacatgtcatttactcatttagacattacattattttttcgtggattcttttcaagtagttcttttcttatct-----

upper sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 4
TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattgagccttcattgtcatccctatttatttactctattcag-taaaacatcctgttctgtggatctgtagaatgatgtatctcttatagaaatt
 ||  | || ||||| ||||| ||||| || || ||||||||||| ||||| ||  ||||||| | ||| || || ||||||||  ||||||||||||||||    | |     |||||  |  | | ||    ||   || |  ||| |   | |  |   | | ||  | ||       || ||| |    |   |  |
CAGTCTTATATTTGAGTATGTGAACAACACGGATTTCAAAGTGCTCTACCCTACACTGACAGACTTTGACATTCGTTACTACATTCATGAGCTACTCAAGgtgagtaattt-ttttcatcttttttcttaaagcttgggtcgacacagattggagactcacgtttctgagtgtgacttgctatctatattcatttttatct

upper sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattgagccttcattgtcatccct-atttatttactctattcagtaaaacatcctgttctgtggatctgtagaatgatgtatctcttatagaaatt
 ||| | || ||||| ||||| |||||||| || ||||||||||| ||||||||  | ||||| | ||||||||| ||||||||  ||||||| ||||||||      | || |||  ||   |  | | || |  ||  | | |  |   ||||||  || |   ||   | ||  |  |    |  |    |  | |  
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgcttggttt-tgtacagaaacatgatgctgattgcgaccgtgtatcgcccaaagtgacgtttagacc

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|163918647|gb|EG711457.1|EG711457
EST:     CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
genomic: CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
EST: gi|29614062|gb|CB619075.1|CB619075
EST:     ATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
genomic: ATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
EST: gi|58676233|gb|CK064920.1|CK064920
EST:     CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCA
genomic: CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCA
EST: gi|58679360|gb|CK068047.1|CK068047
EST:     CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
genomic: CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
EST: gi|29614063|gb|CB619076.1|CB619076
EST:     CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
genomic: CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
EST: gi|218492474|gb|FG956256.1|FG956256
EST:     CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAG                         GCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC
genomic: CCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 60 (downstream exon)
Score: 7

TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattg ... atggccccagGCATTAGACTACTGCCATTCACAAGGCATTATGCATCGAGATGTCAAGCCCCACAATGTTATGATAGATCATGAGCTCCGAAAACTTCGATTGATAGACT




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