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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtccactgtttggtgctcttcaatatcttttgacattgctccttcagtccgtgatatgtttataagcagctatttttacattgacatatgagttgctatcctttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACA

Basic information

species Oryza sativa
transcript LOC_Os08g01740.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 7
------------gtaagtgtccactgttt--ggtgctcttc-aatatcttttgacattgctccttcagtccgtgatatgtttataagcagctatttttacattgacatat-gagttgctatcctttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACA
             |   |  |   || ||  | || | ||  ||||||| |  ||||   ||   |  |  || |  |||       | ||||   | ||| |||  | | | |  ||     ||  ||||||||||||||    ||||||||||||| ||||| || || |||||||| || ||||| || || |||||||| ||||||||||||||||| || || ||| ||
gtacgggtccggttttattactgttgctttggatggtgttggaatatctgtgcacatctatcac-ctttttgttacttgtc-gctgtctgctacagtcacactgatgttttgtgccgcccctattatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAAGGTTCTCGTCCGGCATGACGCGTTGCTTTCAGTTCATCCGACAACAGCA

upper sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G135568_T01 (Zea mays), 3'ss of exon 7
----------------gtaagtgtccactgtttggtgctcttcaatatcttttgacattgctccttcagtccgtgatatgtttataagcagctatttttacattgacatat-gagttgctatcctttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACA
                 | | |||    |       |   |  ||||||| |  ||||   ||     ||  || |  |||   |     ||||     ||| |||  | | | || || |    |   ||||||||||||| ||||||| |||||||| ||||| || ||||||||||| || ||||| || || |||||||||| |||||| |||||||| || || ||||||
gtacggatccggtttcatgactgttgctttggcatggtgttggaatatctgtgcacatctatcgccgcgtttgttacttgtcgctgtat-gctacagccacactgatgttttgtgtcgccactaatatctgctagGGATGAAATGGTGGTGTCACAAGCTATAGAGCTAAACGAAGAGCTACATAAGGTTCTCGTCCGGCATGATGTGTTGCTCTCAGTTCATCCGACAACAACA
















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|29683446|gb|CB679721.1|CB679721
EST:     TAATGCATCTAGTTATGACATCAAG                         GGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
genomic: TAATGCATCTAGTTATGACATCAAGgtaagtgtcc ... ttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
EST: gi|27577615|gb|CB000310.1|CB000310
EST:     CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG                         GGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
genomic: CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAGgtaagtgtcc ... ttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
EST: gi|58602320|gb|CK012848.1|CK012848
EST:     CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG                         GGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
genomic: CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAGgtaagtgtcc ... ttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
EST: gi|66924274|gb|CX111122.1|CX111122
EST:     CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG                         GGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA
genomic: CAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAGgtaagtgtcc ... ttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAA

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), 65 (downstream exon)
Score: 28

GGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAGgtaagtgtcc ... ttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttataagcagctatttttacattgacatatgagttgctatcctttgttgctagGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACA
                     cattgac  putative branch site (score: 28)
                                      ctatccttt  putative PPT
             tatttttacattga  TA-rich tract