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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgtaatgttattgactgttttagtggacgttgcaagtcggtgatgcatttgagtacttgaatcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT

Basic information

species Oryza sativa
transcript LOC_Os05g02880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099317_T05 (Zea mays), 3'ss of exon 3
tggtgtaatgttattgactgttttagtggacgttgcaagtcggtgatgcatttgagtacttgaatcatgatggcttactgtttg--gcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
    |||||||||||||||||||||||||| ||| ||||| |||||||||||||||||||||| |||||| |||||||||||||  |||||| ||   |||||||||| ||||||||||||||||||||||| |||||||||
----gtaatgttattgactgttttagtggaagttccaagttggtgatgcatttgagtacttgactcatgaaggcttactgtttgtggcaaccctttccgcagAATACGAGAAGTGGAGTTGAAGCGCGACTATGCATTTATT

upper sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 2
tggtgtaatgttattgactgttttagtggacgttgcaagtcggtgatgcatttgagtacttgaatcatgatggcttactgtttg--gcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
  |||||||||||||||||||||||||||| ||| ||||| |||||||||||||||||||||| |||||| |||||||||||||  |||||| ||   |||||||||| ||||||||||||||||||||||| |||||||||
--gtgtaatgttattgactgttttagtggaagttccaagttggtgatgcatttgagtacttgactcatgaaggcttactgtttgtggcaaccctttccgcagAATACGAGAAGTGGAGTTGAAGCGCGACTATGCATTTATT
















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|58600797|gb|CK011325.1|CK011325
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88390715|gb|CI609340.1|CI609340
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|33686483|gb|CF314722.1|CF314722
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|218504539|gb|FG956722.1|FG956722
EST:     TCCCGCACTCG-TCTCGTGACCTA-AATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|117248692|gb|CT862835.1|CT862835
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88314811|gb|CI608270.1|CI608270
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88695479|gb|CI737517.1|CI737517
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88724817|gb|CI748076.1|CI748076
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|218501403|gb|FG951125.1|FG951125
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|58681569|gb|CK070256.1|CK070256
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88337350|gb|CI629640.1|CI629640
EST:     TCCCGNACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88352637|gb|CI624576.1|CI624576
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTT
EST: gi|88353004|gb|CI630182.1|CI630182
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88720052|gb|CI745142.1|CI745142
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88395056|gb|CI609372.1|CI609372
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|88314217|gb|CI602549.1|CI602549
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|13420393|gb|AU174483.1|AU174483
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
EST: gi|29655674|gb|CB651949.1|CB651949
EST:     TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
genomic: TCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT

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: 71 (upstream exon), 73 (downstream exon)
Score: 31

GCTATGATGATCGTTATGGAAGCACGCGCTTGTATGTTGGTAGACTGTCTTCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCAGATATGGAAGgtacggacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatttgagtacttgaatcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT
                          ggcttac  putative branch site (score: 31)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtgtaatgttattgactgttttagtggacgttgcaagtcggtgatgcatttgagtacttgaatcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCATTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- -tgtaatg
- - - - - - -ttgactg
- - - - - - - - - - - - - - - - ttgcaag
- - - - - - - - - - - - - - - - - - - - - -tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttg