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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtattctatggacggttgtacagtttcaatttattattccttttgcttttggtggtgccccctgccaatttattatcacttacagtgaaatgcatatgctctcaaatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAGGGAGTGCAGTGAAAGTGGGTTCCACGCCCACCGGGAGACAACGGACGGC

Basic information

species Oryza sativa
transcript LOC_Os01g47262.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47262.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G013625_T03 (Zea mays), 3'ss of exon 7
----------------------------------------------gcaagtattctatggacggttgtacagtttcaatttattattccttttgcttttg-gtggtgccccctgccaatttattatcacttacagtgaaa-tgc---atatgct-ctcaaatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAGGGAGTGCAGTGAAAGTGGGTTCCACGCCCACCGGGAGACAACGGACGGC
                                                || |         ||   || |     |   ||  | ||| ||||||||  |   |  ||   |  |  ||  |  ||| || ||   ||||| |||   || || | |||||||  || ||||  |  ||||||||||||||||| || || |||||||||| ||| |||||||||||    ||||||||||||||| | ||||| ||||||||  |||||
gcaagtgttctttgctaataaatactacacttgtgttacttgtacataaaatggctggcatacatctgcagttcctttgttcttaatttcttttgctcctacattctggttctgggtaaacttatataacgtaatctgaaaatgccctatttgtttctcaaatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAGGGAGTGTGACGAAAGTGGGTTCCACACTCACCGAGAGACAACCAACGGC
















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|44677600|gb|CR291034.1|CR291034
EST:     GTGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
EST: gi|218493474|gb|FG952533.1|FG952533
EST:     ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAGTATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAT
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
EST: gi|33658750|gb|CF281363.1|CF281363
EST:     ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGGTGTGCTTA
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGG-TGTGCTTA
EST: gi|29670555|gb|CB666830.1|CB666830
EST:     ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
EST: gi|88226876|gb|CI224644.1|CI224644
EST:     ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
EST: gi|86496637|gb|CI139270.1|CI139270
EST:     ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG                         GAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG
genomic: ATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAG

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: 66 (upstream exon), 73 (downstream exon)
Score: 158

GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattc ... aatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAGGGAGTGCAGTGAAAGTGGGTTCCACGCCCACCGGGAGACAACGGACGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgccaatttattatcacttacagtgaaatgcatatgctctcaaatcctttagGAACTGTGGAATATTCAGGCTGACAGACCCAGGAGGGATGGGTGTGCTTAGGGAGTGCAGTGAAAGTGGGTTCCACGCCCACCGGGAGACAACGGACGGC
                 cacttac  putative branch site (score: 158)
                                               tccttt  putative PPT
       aatttattatcactta  TA-rich tract