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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacacactacacgaaccctgatccaaattacatcagcaggcagctctgaaaatgcaattttaatcggaaatctgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG

Basic information

species Oryza sativa
transcript LOC_Os10g04860.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 7
---------------------gtatacacactacacgaaccctgatccaa--attacatcagcag--gcagctctgaaaatgcaatttt---aatcggaaatctgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
                      ||   |||  ||| |  |  | | | |   |||   |  |  |  |||| | || |  |  | || |   || | || || | |||    ||  |   ||   |  || | |||||||||| ||| | || ||||| |||||||| || ||| | |||||||| ||||||||||| ||||||||||| || |||||||| ||||| ||||||
gtatccttgatccaaaatacaatactaacagcacaagcgcaattagcaagcgattttgttggaggttgcagatttgcagctaaagttctttaaacctgacattt-cattgggattttgcaaatggtcatcgc-agGTGGAAGTTGATATCCTAACAGGAGCAACCACAATTCTGCGAAGCGACCTGGTGTATGACTGCGGGCAGAGCCTAAACCCTGCTGTAGACTTGGGCCAG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G124175_T01 (Zea mays), 3'ss of exon 2
-------gtatacacactacacgaaccctgatccaaattaca-tcagcaggcagctctg----aaaatgcaattttaatcggaaatc-tgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
        ||| || | | |||||      |    ||   || | |||| ||     ||    |   ||||  |  |||   |     |||  | |  |||| || | | |      ||||||||| | ||||| |||||||| ||||| || || || ||||| ||||| || || || || ||||| ||| |||| ||||||||||| || ||||||
gtaccccttatccaaattgcacgataaagcacagcaagcgcagttagcaagccaaattggtggaggctgcagctcaaattctacccaatgctgacacgtgat-tggaaatttcaacacagGTGGAAATTGATGTCCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGATTTGGGCCAG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 7
gtatacacactacacgaaccctgatccaaattaca-tcagcaggcagctctg----aaaatgcaattttaatcggaaatc-tgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
   ||| |  ||  | |||    ||  |||  ||| | | || || |   ||    |  |||||  || ||||        |||  | |  | || || | | |    | ||||||||| | |||||||||||||| ||||| || || || ||||| ||||| || || || || ||||| ||| |||| |||||||||||||| ||||||
--gtaccccttatccaaactgc-atgaaaagcacagttaacaagccgaattgttggaggatgcagcttcaatcctgcccaatgctgacacct-atttggaaatttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G019799_T01 (Zea mays), 3'ss of exon 7
-------gtatacacactacacgaaccctgatccaaattacatcagcaggc--agctct--gaaaatgcaattttaatcggaaatct-gcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
         || || | | |   |       |  ||||   || | || ||  |  | |  ||   |||| ||| | |     |    ||  | | ||||| || | |        ||||||||||| ||||| |||||||| |||||||| |||||  ||||||||||| |  ||||||| |||||||||||||| ||||| || ||| | ||||||
gtagccctgatccaaattgctatagtaacactgtaaatgcaattaacaagccaaattgttggaggctgcagtttcagttcttcacgaagctgagacatgat-tggaaatgtcatcacagGTGGAAGTTGATGTACTGACAGGAGCAACCACGATCCTACGGAGCGACCTCATTCATGACTGCGGGCAGAGCCTGAACCCTGCAGTAGACCTTGGCCAG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------gtatacacactacacga-accctgatccaaattacatcagcaggcagctctgaaaatgcaattttaat-------cggaaatctgcatatatatg-----atatgaacact----gttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
                                                        |     | || || |  | | ||    | | ||     ||||||          ||  ||||||| |       | || || |   ||| | ||     |||   | |||    ||    |||||||| ||  || | || || || | |||||||||  ||      ||  |  | |||||||||||||||||||| || |||||||| || ||||| |||
gcaagttttttgagattgcctaaaccactttaattattgtttttgttggagttaaattagtgctcttcatgttaacttggagaagactaagcttgcaggcttaatgatgcatcaaattttactatcaaggccgatatatagttatgtgtgtgctaataatgaaactttgagtgtcacagGTGGAGGTAAATCTTCTCACTGGAGAAACCACCATTTTGCAATCTGATATTATATATGACTGTGGGCAGAGCCTCAACCCTGCTGTGGATTTAGGACAG

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|218483070|gb|FG969519.1|FG969519
EST:     CTGACCCGACGTTCACTAGCTACATGAACTATGGAGCTGACACTAGTGAG                         GTGGAAGTCGATGTGCTGACAGGGGCAACCAGCATC
genomic: CTGACCCGACGTTCACTAGCTACATGAACTATGGAGCTGCCACTAGTGAGgtatacacac ... tgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATC




















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: 45 (upstream exon), 71 (downstream exon)
Score: 7

GCAAGCATGGCTAGTGTAAAACTGACGGAGCACGCGTACTGGACCCCTGACCCGACGTTCACTAGCTACATGAACTATGGAGCTGCCACTAGTGAGgtatacacac ... tgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcaattttaatcggaaatctgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG
        ttttaat  putative branch site (score: 7)
                                            ctgttctcc  putative PPT
                          atatatatgatatgaa  TA-rich tract