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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactaccttttccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT

Basic information

species Oryza sativa
transcript LOC_Os07g11000.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G150754_T01 (Zea mays), 3'ss of exon 10
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactaccttttc-cattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
  | | || ||   | | ||       ||||   |   |    |  |         |  |  | | | ||||  |   ||  |||     ||   ||||      |  ||| ||  |  |       |||| | |   |  | | ||   || |||| || || |||||| ||||||| ||||||||||||||||| ||||||||||| |||||||| || || || || || ||||| ||||| || |||| |||
-gtcggttgtgttcagttttaaggcaattttagaaaccagtgctacttttatccgataatcaagagtaaagagtacc-aaccgtggcttctaacctttatgttagaaaatgctcattcagggtcagggtgtataactatgtcatctcatttttcagGCCTGAAGGATCTGGCTGATTTCCTCCCTGCATCTCTTGCTACAATAGTAAGCTACTTTTCCGCTGAGGTGACGCGGGGTGTCTGGAAGCCTGCATCCAT

upper sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G10970.1 (Glycine max), 3'ss of exon 11
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttatt-atttaaccattactatgttc-tatgtgatcatcagtgtttgatactaccttttccatt-ccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
                                                           |  |||  ||     |  | |     |  | | || || ||  | || ||   | |  |    |  ||||   |   | | | | |||   | | ||||| || |||||| |  |||||||||| ||||||||||| || || ||| |||||||||| || || ||||||||  | || ||||||||||| | ||| ||
----------------------------------------------------------ctctaaatatagagcaagagcaaccaaattcatgttcatatagacgttccttgatgcacacaacaatatcatgataccaaaatgcttttcttaataccagGGCTTAAAGATTTAGCTGATTTTCTTCCTGCATCTCTGGCAACCATAATAAGTTACTTCTCTGCTGAAGTAACTAGGGGAGTTTGGAAACCTGTATTTAT

upper sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G28070.1 (Glycine max), 3'ss of exon 11
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactaccttttccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
                                                        |      | |  ||||  |   ||             ||      | ||  | |   | |    ||||| |       || |    | ||  ||  |||| || |||||| |  |||||||||| ||||||||||| || || ||| |||||||||| || || ||||||||  |||| ||||||||||| | ||| ||
------------------------------------------------------tctaaacatagagcaagagcaaccaaattcatgttcatgtagaagttccttgatgtacaccacaatatcatgataccaaaatgcc-tttctttaatatcagGGCTTAAAGATTTAGCTGATTTTCTTCCTGCATCTCTGGCAACCATAATAAGTTACTTCTCTGCTGAAGTAACTAGAGGAGTTTGGAAACCTGTATTTAT

upper sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv07s0104g00390.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactaccttttccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
                                                   ||  |||| || |   |   |    |   |  | ||  ||   |  ||      |||   ||  | ||| |  | ||   ||   ||||    ||| ||| |||| || ||||| ||  |||||||||| ||||| ||| | || || || | |||||||||||| || ||||||||||| ||| |||||||||| || || ||
------------------------------------------------gaaatgattgtatgcaggctctcac--cttctgtttaaattttgg-acatattacacactgattttgacgtgttacttagatctttgcacta----ttctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT

upper sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g02570.t01 (Vitis vinifera), 3'ss of exon 10
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactacctttt-ccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
                                                       | |||  |          |||   | ||  | | | | || ||   |||  || | ||  ||||    ||  ||  |   |   |  |||  |  || |||| || |||||| |  |||||||||| ||||||||| | || || ||  |||||||||| || || ||||||||||||||||| ||||| || |  || ||
------------------------------------------------------gtggttcaatgtggtccccgatcctaaagaaaccatcactaattg-tcatggct-tatttcatgtatatatgtgtaataatttgaaattttcactgtttcagGGCTTAAAGATTTAGCTGATTTTCTTCCTGCATCTTTAGCAACCATTATAAGTTACTTCTCGGCTGAAGTAACACGAGGTGTCTGGAATCCAGTTTTTAT

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|58656218|gb|CK044898.1|CK044898
EST:     TCTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAG                         GTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAA
genomic: TCTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAGgtttgttttt ... tccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAA
EST: gi|88852194|gb|CI683712.1|CI683712
EST:     TCTAACTGCCTGTTCCCATGGAAGACTGTNTCCACGAGAACTGGCTACAG                         GTCTCAAAGATCTGACTGATTTTCTCCCTGCAT
genomic: TCTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAGgtttgttttt ... tccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCAT
EST: gi|29627573|gb|CB632584.1|CB632584
EST:     TTTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAG                         GTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAA
genomic: TCTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAGgtttgttttt ... tccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAA

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: 54 (upstream exon), 63 (downstream exon)
Score: 16

TTACCTGCTTGGGAGATACTGGAAGCTGTTCCATTTGTGGTGGATGCTGCTCTAACTGCCTGTTCCCATGGAAGACTGTTTCCACGAGAACTGGCTACAGgtttgttttt ... tccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattactatgttctatgtgatcatcagtgtttgatactaccttttccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT
                             gtttgat  putative branch site (score: 16)
                                     ctaccttttccattcc  CT-rich tract
                              tttgata  TA-rich tract