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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaatgattggtggaccatctgatcctaa...

Basic information

species Oryza sativa
transcript LOC_Os11g38800.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttc---taat----tctgtatggatctcattgattgtcaataaaatcattattgggctattcttatgg---aggaatgaaatgattggtggaccatctgatcctaa-------------------------------------------------------------------------------------------
|| ||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||||||||| ||   | |     |||  |  |||    ||| |  | || ||||    |         |  | || |   ||||||   | |      | |  || |  |  |||                                                                                           
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatatt-ttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaatgatt---ggtggaccatctgatcctaa----
|| ||  | ||||| ||||||||||||||  | || ||||| ||||||||||||  | |||||||| |||| || |||||||||||||| ||   ||| | |   ||| | | ||| | ||| ||| |         ||  |  |  | | | |    |  ||| |||||    ||| |  || ||||  ||     
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaat---tatagttatcaat-attttcagttttgcttgcatgtgtttggtttcacgttaca--gaattgattctgagtgcagaat-tgattttagacag

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 6
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgtcaataaaa--tcattattgggctatt--cttatggaggaatgaaatgattggtggaccatctgatcctaa
|| ||  | ||||| |||||||| |||||  | || ||||||||||||||||||  | ||||||||||||| ||||||||||||||||| |||  | | | |||   ||| ||| | | ||| |   |   |  |   || |  | | ||   || |   |   ||||||  |   |      ||  |   |  
CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagtttcagtct---tggttctgactaatttttgttccgactttgctaattcggtgttggtttgttctgttttgaaatcttgctttttggctccaactttg-

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G11960.1 (Glycine max), 5'ss of exon 7
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaatgattggtggaccatct---gatcctaa-------------------------------------------------
|| ||  | ||||| || |||||||||||  | || ||||| ||||||||||||  | |||||||| |||| || |||||||||||||| ||   ||   |||  ||| | | | | |  ||||        |  ||| |  |    || | |   | |   ||||  ||  |||    | |   |     ||                                                 
CTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtc---ttcattatagttattaatatttgttttggttttgcttagtcagtgtatcattttcggaataaaaatactttatggtttctttttaggctgcaatctaaaagtttgtgatcatatctcacatttttgtgttatggtgaaacag

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G35750.2 (Glycine max), 5'ss of exon 6
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgt-caataaaatcattattgggctatt--cttatggaggaatgaaatgattggtggaccatctgatcctaa
|| ||  | |||||||||||||| |||||  | || ||||||||||||||||||  | ||||||||||||| ||||||||||||||||| |||  | | | |||   ||| ||| | | ||| |    | |  |   || |  | | ||   || |   |   |||||| ||   |      ||  |   |  
CTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagtttcagtct---tggttctgactaattttattctgatttttctaattcggtgttggtttgttctgttttgaaatcatgcttcttggctccaactttgt

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 5'ss of exon 7
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaat-tctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaat--gattggtgg-accatctgatcctaa-------------
||  | || || ||||||||||||||||| || |||||||||||||||||||||    |||||||| | || |||||  |||| ||||||||  |  || | |  | |   ||   |    || ||   | | || || ||      | ||  |  | |||| |||     |   ||| | |  || |   |||             
CTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgt--tagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G02960.5 (Arabidopsis thaliana), 5'ss of exon 5
----------CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaat-tctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaat--gattggtgg-accatctgatcctaa-------------
          ||  | || || ||||||||||||||||| || |||||||||||||||||||||    |||||||| | || |||||  |||| ||||||||  |  || | |  | |   ||   |    || ||   | | || || ||      | ||  |  | |||| |||     |   ||| | |  || |   |||             
CTTATTTTAGCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgt--tagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

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|163927687|gb|EG710503.1|EG710503
EST:     ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG                         GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
EST: gi|88199974|gb|CI199824.1|CI199824
EST:     ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACTAAGACAG                         GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
EST: gi|87033485|gb|CI188109.1|CI188109
EST:     ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG                         GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC

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: 75 (upstream exon), 74 (downstream exon)
Score: 8

CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCCCAAGGCCATGCCCTTCAGTTCACCATCGCTCCAGACTCCCCCGCCACTC




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