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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG

Basic information

species Oryza sativa
transcript LOC_Os07g07560.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 10
gttagaataattgctt-gacc------tagttcatattcagtccacaaatttggcaa---tttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgcccttt-ttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || ||||||| ||||       |||   | |   ||   |     | || |    | | | |||| |||  |||   | |  |  ||    | | || ||   | | |  || ||    | ||    |   | | |||||||||| ||||||||||| || || || ||||||||| | ||||| |||||||  || ||||| ||||| || || || || || || ||||| |  |
gttaggatgattgctttgaccgcgcagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctga--attgtgtcaactgatgcctga-acatttaacaaggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCTACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCATGGCGGCCACCAACGACCAAGTCG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 15
gttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagc----taacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || |||||||   |        | |   ||        ||     | | | |||| |||  |||   | |  |  ||    | | || || |||  ||||    || || | ||  |   |   | | |||||||||| ||||||||||| || || || || |||||||| ||||| |||||||  || ||||| ||||| || |  ||||| || || ||||| || |
gttaggatgattgctttgaccgcgcagcagt--atctgtg---ctgtgggctcacactcctctga--attgtgtcaactgatgcctga-acatttatttaacaagccatttacccctctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCAGCCACCAACGACCAAGCCG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 15
gttagaataattgcttgacc---tagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || |||||||||||    ||    |||| |  |       |||   |   |||||||| |||  |||  |  |   ||||  |  |   | |  | |  || | |           |  |  || | |||||||||| ||||| ||||| || || || |||||||| |||||||||||||||| ||||||||| ||||| || | ||| || || |||||||| ||||
gttaggatgattgcttgaccacgcaggcattatttatgctgtgtccttgcgtaaccatattcctctga--attgtacca---actgaggcctgagtat-ttaaccaaacaacaacaacaaaaaaactgttgtcagGTTGTAGAGTTGGACTTCCTGTACCCTAGCGAAGGCATTCATCGGCGATGGGAGAGTGGTTACAGGATAACTTCCACAGCGGCCACCAATGACCAAGCTG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 11
gttagaataattgctt-gacc------tagttcatattcagtccacaaatttggcaa---tttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgcccttt-ttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || ||||||| ||||       |||   | |   ||   |     | || |    | | | |||| |||  |||   | |  |  |||   | | || ||   | | |  || ||    | ||    |   | | |||||||||| ||||||||||| || || || ||||||||||| || || |||||||  || ||||| ||||| || |  || || || ||  |||| || |
gttaggatgattgctttgaccgcgtagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctga--attatgtcaactgatgtctga-acatttaacaaggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCCACCGACGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCGGCCACCAACAACCAAGCCG

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|22304710|gb|BQ905932.1|BQ905932
EST:     AATTCGCTGGGGTGTAGTTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         CTTGTAGAATTGGATTTCCTATATCCAAGGTGAAGGCATCCATCGGCGATG
genomic: AA-TCGCTGGGGTGTAG-TTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAA-GTGAAGGCATCCATCGGCGATG
EST: gi|88966779|gb|CI366002.1|CI366002
EST:     GAACTCAGG-TACTCTGAACAG                         G-TGTAGAATTGGATTTCCTATATCCAAATGAAGGCATCCATCGGCGATGG
genomic: GAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
EST: gi|218490208|gb|FG966190.1|FG966190
EST:     GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         GTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
genomic: GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
EST: gi|86866762|gb|CI343562.1|CI343562
EST:     GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         GTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
genomic: GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG

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), 73 (downstream exon)
Score: 49

CAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGCCACCGCTGGAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
                          agctaac  putative branch site (score: 49)
                                cctttttctcatgccc  CT-rich tract
         aatatatctacttat  TA-rich tract