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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcttaattctgtactttcagatatcaatatgcttttttcgttatcatataatatttaatggagcttggtctgaagcaaatgttctctttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT

Basic information

species Oryza sativa
transcript LOC_Os02g10160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10160.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G331374_T01 (Zea mays), 3'ss of exon 2
------tctgcttaattctgtactttcagatatcaatatgcttttttcgttatcatataatatttaatggagcttggtctgaagcaaatgttctctttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT
       || |||| ||| |    |||   |  |       | || |  ||    |  |  |||      |   |  |||| |||   | |   || | ||| ||||| || || || || |||| ||||||  | ||||||||||| |||||||||||||| |||||||||||||||||||| || || || || || || || |
aaattacctccttatttcagacaattcgatttcctgcgcagtattcttatttgtctggagcattcttctaa---ttatctggagc---tatatgctctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT
















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|25803123|gb|CA759084.1|CA759084
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|86492597|gb|CI135230.1|CI135230
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|33681520|gb|CF309759.1|CF309759
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACA
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACA
EST: gi|88539974|gb|CI469974.1|CI469974
EST:     AGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: AGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|88271928|gb|CI387981.1|CI387981
EST:     ACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACAATTCGATAATGGAGCTCCAAAAAGGCAT
genomic: ACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAAC-ATTCGATAATGGAGCTCC-AAAAGGCAT
EST: gi|88849858|gb|CI001564.1|CI001564
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|33658587|gb|CF281200.1|CF281200
EST:     GCTGTCATTTTTGTTGGTGCATCG                         GATGACGGCTACATCCCCAAGCATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|88967505|gb|CI002599.1|CI002599
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
EST: gi|163923351|gb|EG709368.1|EG709368
EST:     GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACG                         GATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG
genomic: GATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGG

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: 29 (upstream exon), 22 (downstream exon)
Score: 1

GCAAGTAAGAGAGAGGTTGCGATCAGTGCTGTCTTTGACTGACGTCACTCGATTTCCAGTGCCAAAGAACCCACAGGCTGTCATTTTTGTTGGTGCAACGgttagtgtca ... ttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatataatatttaatggagcttggtctgaagcaaatgttctctttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT
          atttaat  putative branch site (score: 1)
                                     tgttctctttattttc  putative PPT
     ataatatttaatgga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcttaattctgtactttcagatatcaatatgcttttttcgttatcatataatatttaatggagcttggtctgaagcaaatgttctctttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT

-ctgctta
- - - - -ttctgta
- - - - - - - - - - - - - - - tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaagc