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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtacctgcatctacgtccatcatacatcacctaataacggatcttaatttgtactttgttaaacatagttagtcttctaattgagttatttgctagtcagcgatgggacaaaacagagttaattaactatttctttcttaacatggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g02690.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G068277_T02 (Zea mays), 3'ss of exon 6
gttggtacctgcatctacgtccatcatacatcacctaataacggatcttaatttgtactttgttaaacatagttagtcttctaattgagttatttgctagtcagcgatgggacaaaacag--agttaattaactatttctttcttaacatggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG
||||||||  ||| |   |  |||  || |  |    | ||| | | ||| | | |||     |   |    |   | ||    |||| ||   || |  | || |||  ||  |    |  |  ||  ||  ||| | | | |||   || ||| |||||||| ||||||||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||
gttggtactcgcaacagtgatcatattata--agtgtacaacagttgttactctatacaacagttctctctctatatatt----ttgaattccctg-tgctaagggatttgaagattaggttaactatatatatatatatatattactttgattccagCTATCTGGAGCATCATCTATTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG
















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|88247791|gb|CI247640.1|CI247640
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|89182448|gb|CI113817.1|CI113817
EST:     ATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: ATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86428585|gb|CI075266.1|CI075266
EST:     CGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: CGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86491300|gb|CI133933.1|CI133933
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|163917926|gb|EG714758.1|EG714758
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86426334|gb|CI071431.1|CI071431
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86505602|gb|CI148235.1|CI148235
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACCATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|88248278|gb|CI248127.1|CI248127
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86501777|gb|CI144410.1|CI144410
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|88227499|gb|CI226979.1|CI226979
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|88990699|gb|CI108086.1|CI108086
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|396941424|gb|HO188633.1|HO188633
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|88974820|gb|CI023114.1|CI023114
EST:     AAGAGGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|94362670|gb|CI052789.1|CI052789
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86539112|gb|CI179318.1|CI179318
EST:     GAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: GAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|163926568|gb|EG712432.1|EG712432
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|88221660|gb|CI221616.1|CI221616
EST:     TGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGATACAGTACC
genomic: TGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC
EST: gi|86503019|gb|CI145652.1|CI145652
EST:     AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAG                         CTATCTTGAGCATCATCTCTTGCGTGACACCTAGACCAAGGAAACAGTACC
genomic: AAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACC

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: 58 (upstream exon), 44 (downstream exon)
Score: 6

GATGATCTGAAGAAGACTTGGCTTATTAAAAGGTGCCGGACAATGAATGCTAAATTAAGgttggtacct ... atggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgatgggacaaaacagagttaattaactatttctttcttaacatggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG
                                      tcttaac  putative branch site (score: 6)
                     ttaattaactatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtacctgcatctacgtccatcatacatcacctaataacggatcttaatttgtactttgttaaacatagttagtcttctaattgagttatttgctagtcagcgatgggacaaaacagagttaattaactatttctttcttaacatggttctagCTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA