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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatggctttttgtttttttgttatctcttcgattcgtggctcggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG

Basic information

species Oryza sativa
transcript LOC_Os07g14580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G144618_T01 (Zea mays), 3'ss of exon 1
--------------gtaagatggctttttgttt--ttttgttatctcttcgattcgtggctcggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
               | ||  |      ||| |  ||    |  | ||  |||||||||   |  |  || |  |||||  |  | | ||   |   | |  |    |||| |   || |||| |||||||| |||||||||||||||||||| ||||||||
gtgcgttatgcgtgctcaggcgcgcgcctgtctgattcgcctgaccctgtgattcgtgg--tgaataatttggctggtt--ggaccttattgtgtgctcgtgttgcgtgtttta--tgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG

upper sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 1
gtaagatggctttt-tgtttttttgttatctcttcgattcgtggctc--ggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgt-tgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
||  | |  | |    |  | | || |    | |      |||  ||  |  ||      |||| |   ||   | | |   | ||  |   ||   |||  | |||||||||||||||| ||||||||||||||||| || ||||||||
gtgcgttcccctgcgcgcctgtctgattcaccctgaccctgtgattcctgtgtgaacaatttggctggttggaccttatttgtgtgctcgtgttgcatgttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
















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|33675101|gb|CF303340.1|CF303340
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|117230076|gb|CT853782.1|CT853782
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|88724679|gb|CI747938.1|CI747938
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|33657056|gb|CF279670.1|CF279670
EST:     CCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|88358340|gb|CI606849.1|CI606849
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|58597046|gb|CK007574.1|CK007574
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|86900903|gb|CI304108.1|CI304108
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTT
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTT
EST: gi|86596782|gb|CI286695.1|CI286695
EST:     CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: CCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
EST: gi|58690454|gb|CK079141.1|CK079141
EST:     TCGACACCAACCTCAACCAGTGG                         AGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
genomic: TCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG

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: 20 (upstream exon), 41 (downstream exon)
Score: 3

CATCACCGTGCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGGCCACGTCACGCTCTACGACTTCGACACCAACCTCAACCAGTGGgtaagatggc ... gtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
                                 gcctgat  putative branch site (score: 3)
                                      atttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatggctttttgtttttttgttatctcttcgattcgtggctcggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG