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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaatagggtcccaaactctatccagaaagttctgatagtttaagactcacaggagtttgctttgttaggtgtgaacttcacaatgcatgaatttcatg...

Basic information

species Oryza sativa
transcript LOC_Os03g31550.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G050984_T01 (Zea mays), 5'ss of exon 5
TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaatagggtcccaaactctatccagaaagttctgatagtttaagactcacaggagt-ttgctttg---ttaggtgtgaacttcacaatgcatgaatttcatg
  ||| | ||||||||| ||||||||| ||||| ||||| || ||||| ||| |||| || || ||||| |||||||||||| ||||||||||||||||||||| |        || ||||  ||||    |  | | |  ||     |    ||| |  || |||    |||| | |||  ||    |||||||||  |  | 
CATAAATAATTTTAACAGTAATAACCGCTGGAGGAAGCGAGGAATTGCCATGATTCCGACAAAATTTGGCATATCCTTCACTGCAAAATTCATGAATCAGgtga-tccaccatgaagctctg-ccagtctatcattacaaattggagtttgtgggattactgatttccttttagttttgatatttg--atgcatgaaaattctt

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA15G03870.1 (Glycine max), 5'ss of exon 9
TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaa---tagggtcccaaactctatccagaaagttctgatagtttaagactcacaggagtttgctttgttaggtgtgaacttcacaa--tgcatgaatttcatg
 ||     | || || | | | ||||| ||||| |||||||||||||||||| |||| |  |||||||| |||||||| || |||||  | ||||| ||||| ||   |    ||    | |||||    |   || | | | |  |  |   | ||   |||    || |   |  | |  | | ||  |     | |||  ||
AGTTGACCAATTCAATAGTCACAACCGCTGGAGGAAGCGTGGCATTGCTATGATTCCTAATAAGTTTGGTATATCCTTTACAACAAAGCTTATGAACCAGgtaaaatctgaattctatcattctattttaa---ttttaaaaatgaagaaa--aaagtgatttcaactgatgtttaaggaaataagaagcttgtcaagttttgtg

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G41520.1 (Glycine max), 5'ss of exon 10
TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaa--tagggtcccaaactctatccagaaagttctgatagtt-taagactcacaggagtttgctttgttaggtgtgaacttcacaatgcatgaatttcatg-
 ||    || || || | | | ||||| ||||| |||||||||||||||||| |||| |  |||||||| |||||||| || |||||  | ||||| ||||| ||    |  | |  || |||||    |   |    | ||   | |   | || | | |||        |  |  |||  |    | |  ||  ||  ||  
AGTTGACGAATTCAATAGTCACAACCGCTGGAGGAAGCGTGGCATTGCTATGATTCCTAATAAGTTTGGTATATCCTTTACGACAAAGCTTATGAACCAGgtaaaatctgaattcataattctattttaattttaaaaaaagaggtgattttaactgaaattta----aggaaataagaagcttgtcaggtttgttttatattt

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 5'ss of exon 9
TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtga-----atagggtcccaaactctatccagaaagttctgata---gtttaaga-ctcacaggagtttgctttg--ttaggtgtgaacttcacaat-gcatgaat-ttcatg---------------------------------------------------------
 |     || ||||| | | |||| || |||| |||||||||  | |||||||||||||| || ||||| |||||||| || ||||| |||||||||||||| |      |  | |   || |  | ||    || ||  | ||   ||  | || || | | || |  |||     ||   ||  ||  |||| || |||  |   ||||                                                           
AGCGGACGAGTTTAATAGTCATAATCGGTGGAAAAAGCGTGGTGTAGCTATGGTTCCCACAAAATTTGGCATATCCTTTACCACAAAGTTCATGAATCAGgttatctttgtttgatgtgaatccttttctttcaaatttagttatctgtcgaggaactgaaaagattaagctaaagcttccttggaaatctcaccattgcactaccgttcaaagctagaatctgaattttgagatacttaatccaatatataattaaacggctgtcacag

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G34890.1 (Arabidopsis thaliana), 5'ss of exon 9
TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtga----------atagggtcccaaactctatccagaaagttct-----gatagtttaagactcacaggagtttgctttgttaggtgtgaacttcac-aatgcatga--atttcatg---------------------------------------------------------------------
 |     || ||||| | | |||| || |||| |||||||||  | |||||||||||||| || ||||| ||||| || || ||||| |||||||||||||| |          | | ||  ||    ||| || ||  |||| |     || |   |   ||  | | |||     | ||  |  ||  || ||| | ||||||  |  ||| | ||                                                                     
AGCTGACGAATTTAATAGTCATAATCGGTGGAAAAAGCGTGGTGTAGCTATGGTTCCCACAAAATTTGGCATATCATTTACCACAAAGTTCATGAATCAGgttatctttggttgacatggatcctttttctttcaagttagttatctgtcgagaaactggaaca-ataagagaa-aatctgcca--tggaaatttcgccaatgcactaccattgcttgcaaagctagaatctaaattttaaaatacttatcttttatttttccctccacattatggggatgttacag

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|58682426|gb|CK071113.1|CK071113
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|58695695|gb|CK084382.1|CK084382
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|218495632|gb|FG967039.1|FG967039
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|29675056|gb|CB671331.1|CB671331
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|58683895|gb|CK072582.1|CK072582
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT

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: 74 (upstream exon), 59 (downstream exon)
Score: 51

TGTAATTGATTTTAACAATAATAACCGTTGGAGAAAGCGTGGCATTGCTATGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG




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