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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcag

Basic information

species Oryza sativa
transcript LOC_Os09g32680.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
ACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcag
 || || ||||| ||| | |||||||| ||||| || || ||| | ||||| |||||||  ||    |||||||||||||||||||||||||||||||| |||||     || ||      ||| | |   || ||||    |  ||    | | ||| | | |||| |||          | | | |      |||||| |||
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagttctatta-----ttggttt---cccggctat--ttattc---tgtattgttttcttcaccca----------actctgtgacttgcaattcccag
















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|38568817|gb|CD671032.1|CD671032
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTC-GTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTT-GGACTTCTATGACACCTACA-GATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|24468776|gb|CA305725.1|CA305725
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|86493556|gb|CI136189.1|CI136189
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|29660228|gb|CB656503.1|CB656503
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|29660227|gb|CB656502.1|CB656502
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|218503593|gb|FG957186.1|FG957186
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|88833089|gb|CI369979.1|CI369979
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|88258947|gb|CI363240.1|CI363240
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|27547661|gb|CA765583.2|CA765583
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACNAGGAT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAG-AT

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: 72 (upstream exon), 72 (downstream exon)
Score: 59

ACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATTGATCCTCAAAGAGGGCTCCCAGAGGACAAAATAGCCCCTGTGATGAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT