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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaaatctgtaagctcttgtctttatccaataagcaacatatatgcatgataatacatacataatccacgcagacaactatagtctacatatttcaagtgaaacagcagcacccaactctgtttattggaggtgatcctcactgacaagatatacattttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGATCTTGGGTTGTACGTGTTCGCGTCCAAGCCGTCGAGTGGAGCAGCCATAT

Basic information

species Oryza sativa
transcript LOC_Os03g61710.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G458549_T01 (Zea mays), 3'ss of exon 12
gtaaattaaatctgtaagctcttgtctttatccaataagcaacatatatgcatgataatacatacataat-ccacgcagacaactatagtctacatatttcaagtgaaacagcagcacccaactctgtttattggaggtgatcctcactgacaagatatacattttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGATCTTGGGTTGTACGTGTTCGCGTCCAAGCCGTCGAGTGGAGCAGCCATAT
                                                            ||  ||   |  |  |   ||||||  |||      | |   |  |     ||| |  |    | | ||| |    ||     ||    |     ||    |||||   |||||||| |||||| ||||||||||| ||| ||||||| ||||| |||   ||| | ||  | ||||||||||| |||||||||||||| || || |||||| 
-----------------------------------------------------------gcaagcaagctgtcttgtttacaactggagt------agtgtgatggtgcatgcatcctctgtttttctttctccatggcttggctt-tggctctaatgcttatttttacgcagGAAATGTACTACAAATCAAGGATTGACAGGGGAGTAATCAAGCAGGGCGATGTGGGCCTATACGTGTTCGCATCCAAGCCGTCGAGCGGCGCGGCCATAC
















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|38565679|gb|CK085132.1|CK085132
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|55409316|gb|CV721692.1|CV721692
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|218499430|gb|FG950945.1|FG950945
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAAGATCGACCGGGGAGTGATCAA
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAA
EST: gi|14191716|gb|AU183927.1|AU183927
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|86878627|gb|CI340549.1|CI340549
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCCCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|38565696|gb|CK085149.1|CK085149
EST:     TCGCTTGGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|38565610|gb|CK085063.1|CK085063
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|38565704|gb|CK085157.1|CK085157
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|88542084|gb|CI471392.1|CI471392
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGGGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
EST: gi|87006813|gb|CI285847.1|CI285847
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAAT
EST: gi|218498226|gb|FG955584.1|FG955584
EST:     TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAG                         GAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT
genomic: TCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGAT

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: 68 (upstream exon), 72 (downstream exon)
Score: 44

CGGAGCACTCGGAGCACGTCTTACTGGAGCAGGGTGGGGTGGCTGTGCAGTCGCTTTGGTTAAGGAAGGCATTGTCCCGCAGTTTATTCTCAATTTAAAGgtaaattaaa ... tttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGATCTTGGGTTGTACGTGTTCGCGTCCAAGCCGTCGAGTGGAGCAGCCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaactctgtttattggaggtgatcctcactgacaagatatacattttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGATCTTGGGTTGTACGTGTTCGCGTCCAAGCCGTCGAGTGGAGCAGCCATAT
                           cactgac  putative branch site (score: 44)
                                            ttttatt  putative PPT
                                  aagatatacattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaaatctgtaagctcttgtctttatccaataagcaacatatatgcatgataatacatacataatccacgcagacaactatagtctacatatttcaagtgaaacagcagcacccaactctgtttattggaggtgatcctcactgacaagatatacattttattgcagGAAACGTACTATAAATCAAGGATCGACCGGGGAGTGATCAACCAGAAGGATCTTGGGTTGTACGTGTTCGCGTCCAAGCCGTCGAGTGGAGCAGCCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG