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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g06440.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 9
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  |   | |||  | |  | | | | | || || |||  ||| || |     | || |  |||  |  |||||||||||||||||| || |||||| ||||||||||| ||||||| |||||| | |||| |||||||||||||||||| |||||
ttactgggagctgaactcgtcagacttatctgttactcgaatttt-tattctcacatgaatcttgcccccagaaaatttgac--tcggagct--atcggtttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G894029_T01 (Zea mays), 3'ss of exon 19
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  | | | |||  | |  | | | | | || || |||  ||| || |    || || |  ||| ||  |||||||||||||||||| || |||||| |||||| |||| ||||||| |||||| | |||| |||||||||||||||||| |||||
ttactgggagctgaactcgtcagacttatctgttactcaaatttt-tattctcacatgaatgttgcccccagaaaatttgac--ttggagct--atcgatttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGAAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G081668_T01 (Zea mays), 3'ss of exon 3
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  | | | |||  | |  | | | | | || || |||  ||| || |    || || |  |||  |  |||||||||||||||||| || || ||| |||||| |||| ||||||| |||||| | |||| |||||||||||||||||| |||||
ttactgggagctgaactcgtcagacttatctgttactcaaatttt-tattctcacatgaatgttgcccccagaaaatttgac--ttggagct--atcggtttcagGCAAGTTCTTGAGGTAGTGGCGGGAAGCAAAGAAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G137367_T01 (Zea mays), 3'ss of exon 13
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  | | | |||  | |  | | | | | || || |||  ||| || |     | || |  |||  |  |||||||||||||||||| || |||||| | ||||||||| ||||||| |||||| | |||| |||||||||||  ||||| || ||
ttactgggagctgaactcgtcagacttatctgttactcaaatttt-tattctcacatgaatgttgcccccagaaaatttgac--tcggagct--atcggtttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGAAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCGTAACACATGTAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G704381_T01 (Zea mays), 3'ss of exon 4
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  | | | |||  | |  | | | | | || || | |  ||| || |     | || |  |||  |  |||||||||||||||||| || |||||| ||||||||||| ||||||| |||||| | || | |||||||||||||||||| |||| 
ttactgggagctgaactcgtcagacttatctgttactcaaatttt-tattctcacatgaatgttgcccctagaaaatttgac--tcggagct--atcggtttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGCAGAACTCTGTACCACAACACATGCAT

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G058862_T02 (Zea mays), 3'ss of exon 3
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
      | |  |||  || ||| ||||  || ||  | | | |||  | |  | | | | | || || | |  ||| || |     | || |  |||| |  |||||||||||||||||| || |||||| ||||||||||| ||||||| |||||| | |||| |||||||||||||||||| |||||
ttactaggacctgaactcgtcagccttacctgttactcaaatttt-tattctcacatgaatgttgcccctagaaaatttgac--tcggagct--atcagtttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G384762_T01 (Zea mays), 3'ss of exon 9
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  || |||  ||| ||| ||  | | | |||  | |  | | | | | || || |||  ||| || |     | || |  |||  |  |||||||||||||||||| || |||||| ||||||||||| ||||||| |||||| | |||| |||||||||||  ||||| || ||
ttactgggagctgaactcgtcagacttatctgttactca-attttttattctcacatgaatgttgcccccagaaaatttgac--tcggagct--atcggtttcagGCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCGTAACACATGTAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G051032_T01 (Zea mays), 3'ss of exon 11
-----ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
     || |  |||  |  |||  ||| ||| ||  | | | |||  | |  | | | | | || || | |  ||| || |    || |  |  |||  |  |||||||||||||||||| || |  ||| ||||||||||| ||| | | |||||| | |||| |||||||||||||||||| |||||
ttactgggagctgaacttgtcagacttatctgttactcaaatttt-tattctcacatgaatgttgcccctagaaaatttgac--ttggaact--atcggtttcagGCAAGTTCTTGAGGTAGTGGTCGGAAGCAAAGGAATTTCTGGCGTAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 10
ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaa--taactgaagat-acatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
   | || |  ||   ||    ||   |   || | | ||     || |  |  | |     |  |  | | || |  || |||    | |  ||    |||||||||||||||||||||||||||| || |||||  |   |||||| |||    |||| || ||| ||||| ||||||| |||||
tatatttaaggtctctaag---ttaagtcacttgttccttttgtgtgtgtttttcctcaaaatttataatactttaattatctgttccttaagtcgtctccagGCAAGTTCTTGAGGTTGTAGCTGGCTGTAAAGGTGTCAGTGACATAGAACAACTAAGCAAGACTTTGTACAACAACACCTGCAG

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|58695600|gb|CK084287.1|CK084287
EST:     TACGAGCCGGATTCTACAGTAAAAGGTCGCAATGAGCCCTGCTTAGTCAG                         GCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGG
genomic: TACGAGCCGGATTCTACAGTAAAAGGTCGCAATGAGCCCTGCTTAGTCAGgtaattcaac ... tcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGG
EST: gi|86901885|gb|CI298532.1|CI298532
EST:     TACGAGCCGGATTCTACAGTAAAAGGTCGCAATGAGCCCTGCTTAGTCAG                         GCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGG
genomic: TACGAGCCGGATTCTACAGTAAAAGGTCGCAATGAGCCCTGCTTAGTCAGgtaattcaac ... tcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGG

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: 44 (upstream exon), 67 (downstream exon)
Score: 12

CTGGAATCAAGTTCGTGAAGTCTGTCTGGCCATCCAAGAAGAAAGAAAAGTACGAGCCGGATTCTACAGTAAAAGGTCGCAATGAGCCCTGCTTAGTCAGgtaattcaac ... tcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG
                            taataac  putative branch site (score: 12)
                    aagaaaattaataact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaattgatttcatcaaccttttcttttgtttatactttacacttgcgcctaactttttcctccaagaaaattaataactgaagatacatcaatcccagGCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - cttttgt
- - - - - - - - - - - - - - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa