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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaaaggaaactgtttttagatccatgaattataacttgtttcttgtattgtcattctaaattgtttgaattttacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
gtcaaaggaa-actgtttttagatccatgaattataacttgtttcttgtattgtcattctaaattgtttgaattttaca----caacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
|| |||  ||   |||||| ||||  ||  | | |   |  |  ||| || | | |||  ||  || ||||  ||||       || |||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| |
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
---------------------gtcaaaggaaactgtttttagatccatgaattataacttgtttcttgtattgtcattctaaattgtttgaattttacac-----aacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
                      | |    |   | | ||    |  |||   | | |  ||| |     | |   ||| |||||  | |   | ||  |      || |||||||||| |||||||||||  | ||||| || |||||||||||||  ||||||||||| || ||||| ||  |||| |||||| | || | ||| || |
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgttactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
--------gtcaaaggaaactgtt-------tttagatccatgaattataacttgtttcttgtattgtcattctaaattgtttgaattttacac------------aacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
         ||  | | |||| ||       ||||||| ||||  | ||    |||    | ||||   |   |  ||| |    ||| ||               || |||||||||| |||||||||||  | ||||| ||||||||||||||||  ||||||||||| || ||||| ||  |||| |||||| | || | ||| || |
gtttcattttcttatgcaacttttcttttattttagattcatgcgt-atggtatgtgatctttattactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtcaaaggaaactgtttttagatccatgaattataacttgtttcttg----tattgtcattctaaattgtttgaattttacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
             |   |   |   | | |  || ||     ||| |  | ||   |       |  |  || | | ||      ||| | |  |   ||||||||||| || |||||||| || ||||| ||||||||||||||||| ||  | || ||||| ||||| || || ||||||||| |||| |  || ||  
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctg-attccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gtcaaaggaaactgtttttagatccatgaattataacttgtttcttgtattgtcattctaaattgtt---tgaattttacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
               ||  |  ||  | ||    |  |  |   || ||   | |   ||  | |  | |  || ||||     || || |   |   |||||||| || || ||||||||||||||||| ||||||||||||||||| ||| | || || || || |||||  | || || || ||||| |  |||||  
tgcattgtgccaagatcttatcaacattttgcatgcactgtattttctatactttcagttacagtcacgtattatattgacgagtgcatctctgatg-cagGTTATTATTGTAACAAGCTCATTAATGAAGGATATGAACAGCAAGACAGATCTTTATCGCGCGAACGCTATACGGGTCCTCTGCAGAATCACAGATGGTG

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S53_204V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtcaaaggaaactgtttttagatccatgaattataacttgtttcttgtattgtca---ttctaaattgt-ttgaattttacacaac------agGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
        |   |   |     ||  |||   | ||| | |  ||  |  | || | || |   |||   | | | |||||    |||   |      |||| || || || |||||||| |||||||| |||||||||||||||||  |  | || ||||| || || ||  | || || || ||||| |  || ||  
acggcacgctttgttcatgtcattccgatatgtcaataacagttttctgttcgtttagttaggattcagtactttattgaagggcacaactctgatgtagGTAATAATCGTAACAAGCTCCTTAATGAAGGATATGAACAGCAAGACAAACCTTTATCGTGCAAACGCCATACGGGTGCTCTGCAGAATCACAGACGGTG

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|88443658|gb|CI591883.1|CI591883
EST:     GGCGGGTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
EST: gi|88454333|gb|CI569905.1|CI569905
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
EST: gi|88333728|gb|CI643760.1|CI643760
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGATA
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATA
EST: gi|88405887|gb|CI591282.1|CI591282
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAA
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAA
EST: gi|88328220|gb|CI651227.1|CI651227
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGAT
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGAT
EST: gi|88311189|gb|CI570263.1|CI570263
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
EST: gi|88370130|gb|CI585135.1|CI585135
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGAT
EST: gi|88310289|gb|CI659079.1|CI659079
EST:     GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAG                         GTTATCATAGTCACAAGCTCATTAATGA
genomic: GGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGA

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: 72 (upstream exon), 74 (downstream exon)
Score: 43

AGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCACCATCATCAGATGAGgtcaaaggaa ... tacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attataacttgtttcttgtattgtcattctaaattgtttgaattttacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA
                          ttctaaa  putative branch site (score: 43)
                         attctaaattgtttga  TA-rich tract