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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC

Basic information

species Oryza sativa
transcript LOC_Os01g54100.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 6
gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
         |||||||    | |  ||   |    | || |  || | ||| |||  |  ||||||||  |    ||   | |  ||| |||| ||| |||||||||||||||||||| ||  ||| |||||| | ||||||||||||||||||||||   || ||||| ||||| |||||||||||
--------gtaaagca----gctaaagc-ttgcagcagtgtcttagtatatgaatattcttttgacta--tagttatatctatccagGCACAAAGTACACACAACAATCCTACAAAGTTAGCAATAGTTTCCCCTACAAATGGATAAACAAGAAATGGCAAGATGGTTTCTATGTAACTTCCATGGC

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
gtaaccagttaaagcatgctgtttcagtgctattcctgtc-ttataatgtataaattattctttgactaactt-agcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
|||  |  ||     |  |  ||| | |||   |       ||||      |  ||   | ||| ||    || | |||   | || ||| ||   ||||  |||||||||||||||||| |||||| |||| || ||||| |||||||| || || |||||||| || |||||||| || || |||||
gtattc--ttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgctt--ttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
      |||  || |||  |       ||  ||| || |   | ||| |||    |||  ||||  | ||||    |  ||   |  ||| |||   ||    ||||| || |||||||| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| || || |||||
---gttagtctaa-catatttggctgatgg-atttctatgacaaaatttat---ctatattttgcttgacttcatttcattgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
                          ||  | |  ||||  | | |||    | |     | |  || ||      | |      ||| |||   || || |||||||| |||||||| || ||| | || || ||||| ||||| ||||| || |||||||| || ||||| ||||||||||||||
--------------------------gtattgtcgctgttat-tgatg-gccactggcattgtcgctgacgcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
                          ||  | |  ||||  | | |||    | |     | |  || ||     || |      ||| |||   || || |||||||| |||||||| || ||| | || || ||||| ||||| ||||| || |||||||| || ||||| ||||||||||||||
--------------------------gtattgtcgctgttat-tgatg-gccactggcattgttgctgacgcgtgattcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|29687708|gb|CB683983.1|CB683983
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|218496998|gb|FG950841.1|FG950841
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|29687566|gb|CB683841.1|CB683841
EST:     GGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: GGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|218494323|gb|FG952810.1|FG952810
EST:     TTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|58688056|gb|CK076743.1|CK076743
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATA
EST: gi|29625957|gb|CB630968.1|CB630968
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|163919775|gb|EG710337.1|EG710337
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|58591468|gb|CF989776.1|CF989776
EST:     CTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATGGTTTCCCTTTCA
genomic: CTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
EST: gi|38565581|gb|CK085034.1|CK085034
EST:     TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG                         GAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA
genomic: TGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCA

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: 56 (upstream exon), 70 (downstream exon)
Score: 50

GAATGGATTATGGACCAATGGGAAAGGAACTACTATATAACTGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAGgtaaccagtt ... gcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
                               gactaac  putative branch site (score: 50)
                                            tgctttttt  putative PPT
        ttataatgtataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccagttaaagcatgctgtttcagtgctattcctgtcttataatgtataaattattctttgactaacttagcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG