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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcagcttgtctaacaattgtcaaataacataaggtaacataagaaaaacatcacagtaaaactcaaatgtttctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG

Basic information

species Oryza sativa
transcript LOC_Os07g14850.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G082580_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------------------------------------gtattgtcagcttgtctaacaattgt-caaataacataaggtaacataagaaaaacatcacagtaa-aactcaaatgtttctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG
                                                                                                     |  |||   |||  ||| |  ||||  ||||     || | |           |  | ||| |    | | | ||    || | || |||| || || |  || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||  | ||||| |||||
gtgttgtcaacctttcaaacatagcttacaacagcaccgttagagttcaaaggcatattcttagatataaaaaaccaggacagttcttctgttaatccatttcatgttgacttcactacctgttgtgtaaatggatgaaagcatttctgtttctatttgacacttgtgaataacattgcactgttctccagGTGCAGATATTGAGAAGGCTGGAATTGTAAATCAACAGAAACTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCGACACTTCTTGAGAATGG

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------------------------------------------gtattgtcagcttgtctaacaattgtc--aaataacataaggtaacataagaaaaacatcacagtaa-aactcaaatgtttctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG
                                                                                                  |  ||||  |||  ||| |  ||||   |||      |  | |           |  | ||| |   || | | || |  || | || |||| ||||| |  || || || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||||  | ||||| || ||
gtactgtcaacctttcaaacatagcttacaacagcaccgctagagttcaaaggcatatgcttagatttcaaaaaccaggacaatcctgttcaaccatttcctgtcgacttcactacctgttgtgtaaaagggaggagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 11
----gtattgtcagcttgtctaacaattgtcaaataaca----taaggtaacataagaaaaacatcacagtaa-aactcaaatgttt--ctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG
      ||  | |  |    |     || ||| |||       |    ||| | |    |     | || |   || |  | | |||  || |  |  |||   |||||  || ||  |    ||  ||  | |   |||  | || ||||| |||||||||||| |||| ||||||||||||||| | |||||  ||||
aaaaccatgattacttcaatttgttgttatcacatattcctttttgcataatacattctatttgcctcacttctaattttattatttaactgtcatatagGGATTGAGAGTGAGAAGTCAACTATGTTGTCTGAGACGAAATTGGAGAAGAAGTTTGGGCAGTCTCCTGTGTTTGTTGCATCAACTCTTCTTGAGGATGG

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|427599|gb|D23732.1|D23732
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGGATTGTGAATCAACAGA-GCTAGAAA-GA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|396941331|gb|HO188540.1|HO188540
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58664382|gb|CK053068.1|CK053068
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58610601|gb|CK038313.1|CK038313
EST:     TGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: TGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58673459|gb|CK062145.1|CK062145
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|29685626|gb|CB681901.1|CB681901
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|427628|gb|D23761.1|D23761
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|38473343|gb|CF957475.1|CF957475
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAANAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA

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: 70 (upstream exon), 54 (downstream exon)
Score: 32

ACAAAACCTAAGCCGGAGAAAAAGAAAAGACTGTTTTTCAAGAAAGCAGAAAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaggtaacataagaaaaacatcacagtaaaactcaaatgtttctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG
   aggtaac  putative branch site (score: 32)
                                         tttctttact  putative PPT
      taacataagaaaaa  TA-rich tract