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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcctgtctttctaccacacacttcttcattgttggctagtatctggagaacaggcttacctgttttttgcgggatctgggcccgaataccacaaactcgtagaagtgtgtgaactgattagtttatttctctgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTATCTCTTGTGATGATGACAATATACCCCATCGTGATAGCACCTCTGTTCA

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 6
------------------gtatctcctgtctttctaccacacacttct--tcattgttggctagtatctggagaacaggcttacctgttt--tttgcgggatctg-ggcccgaataccaca---aactcgtag-----------aagtgtgtgaactgattagttta--tttctctgtgct---tcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTATCTCTTGTGATGATGACAATATACCCCATCGTGATAGCACCTCTGTTCA
                   | | |      |   ||    ||| || |  |||        || | ||    || | |  ||    |||   ||| |  | ||         || | ||||   ||||  | |           |||||  | ||||||||  || |  ||| |||||  |   ||||| |||||| || |||||||| |||||||| |||||||||||||||| |||| ||||  |||||||||||||||||||||| |||||||| ||||||||||
gtaagtcctcttattctattgtttgaaagttacttaattaacaattatgttcacaacaaattattttcctttgacctgttttgttagttcggtttccaaggtccacaaattcaaaatcacatgtaacttatggtagcgtcacctaagtgcatcaactgattctttcaattttttctgtattctttcagATTGGAGGACCTTACCTGGCTATATATCTCTGGGGTTTTATGTTTGTATTAGCTCTACTGATGATGACAATATACCCCATTGTGATAGCTCCTCTGTTCA

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 6
gtatctcctgtctttctaccacacacttcttcattg-ttggctagtatctggagaacaggcttac---ctgttttttgcgggatc---------tgggcccgaataccacaaact------cgtagaagtgt---gtgaactgatt------agttta----tttctctgtgct---tcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTATCTCTTGTGATGATGACAATATACCCCATCGTGATAGCACCTCTGTTCA
||| |||||  | |||||      |    || |||  ||  | | ||| || |    |      |   || || |||   || |          |      |   || ||| | |      | | ||  |||   || |  || ||       ||  |    ||| |||||  |   ||||| |||||| ||||||||||  |||||||| |  |||||||||||||||||| ||||| |||||||||||||||||||||| |||||||| ||||||||||
gtaactcct--cgttctattgtttaaaggttaattaattaacaattatgtgcaaggtaactcctcgttctattgtttaaaggttaattaattaataattatgtgcacaacatatttttcccctttgacctgttttgttagttggttttacaaggtccacatttttttctgtattctttcagATTGGAGGACCCTACCTGGATATATATCTCTTTGGTTTTATGTTTGCATTAGCTCTTCTGATGATGACAATATACCCCATTGTGATAGCTCCTCTGTTCA
















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|88578235|gb|CI687155.1|CI687155
EST:     CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG                         AATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA
genomic: CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAGgtatctcctg ... tgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA
EST: gi|58678409|gb|CK067096.1|CK067096
EST:     CCATCTTACTTGGACCTCCTATNGTGGCTGCTATTATCATCATAGTACAG                         AATGGAGGGCCCTACCT
genomic: CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAGgtatctcctg ... tgtgcttcagAATGGAGGGCCCTACCT
EST: gi|58589625|gb|CF987933.1|CF987933
EST:     CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG                         AATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA
genomic: CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAGgtatctcctg ... tgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA
EST: gi|88328438|gb|CI676643.1|CI676643
EST:     CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG                         AATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA
genomic: CCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAGgtatctcctg ... tgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTA

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), 74 (downstream exon)
Score: 20

CAAACTATTTGGCTCTTCATTAGGGACATGATCAAAGGGATTTTGCTATCCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAGgtatctcctg ... tgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTATCTCTTGTGATGATGACAATATACCCCATCGTGATAGCACCTCTGTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacaaactcgtagaagtgtgtgaactgattagtttatttctctgtgcttcagAATGGAGGGCCCTACCTGGCAATATATCTATGGGGTTTTATGTTTGCATTATCTCTTGTGATGATGACAATATACCCCATCGTGATAGCACCTCTGTTCA
                         aactgat  putative branch site (score: 20)
                                       tttctctgtgcttc  putative PPT
                            tgattagtttattt  TA-rich tract