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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgcagtgaccaagttaattgattggttttctggaaattcatacacaatcagcacctcaccatatttttctgttttctgatttctcaaaacaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATAAATGGACCCATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGC

Basic information

species Oryza sativa
transcript LOC_Os01g73120.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147709_T01 (Zea mays), 3'ss of exon 5
ttcgcagtgaccaagttaattgattggttttctggaaattca-tacacaatcagcacc-tcaccatatttttctgttttctgatttctcaaaacaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATAAATGGACCCATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGC
 |   |    |    | || | |    |||  | ||||  || |  || ||     |  |      | |||    | ||||||||| ||||| || |  |||||||||||||||||||||| || |||||||| || || ||| |||| || || ||||| ||||| |||||||| |||||||||||||||||||||  |||
-ttttacctccttgctaaagttaggaatttcttcgaaacacaatttactatggatccaatttatgcaatttggattgttctgatttgtcaaacca-tctcagGATTTTACCTCCTTGCTAAAGTGGAAGAGGCTGCTGACAAAACTATCTACAATTGGACTCATCAGATTGTTAGTGGTCATACTCTTAAGCATCTATGTGC
















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|22306364|gb|BQ907586.1|BQ907586
EST:     TATACACACTTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TATACACA-TTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29668922|gb|CB665197.1|CB665197
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|218501560|gb|FG959366.1|FG959366
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTATGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29661521|gb|CB657796.1|CB657796
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|33654477|gb|CF277091.1|CF277091
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|427638|gb|D23771.1|D23771
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29661520|gb|CB657795.1|CB657795
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|157651623|gb|EX451257.1|EX451257
EST:     TGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29668921|gb|CB665196.1|CB665196
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|27578313|gb|CB001008.1|CB001008
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|88959711|gb|CI002321.1|CI002321
EST:     TTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29671029|gb|CB667304.1|CB667304
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAG                         GATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATA
EST: gi|29671028|gb|CB667303.1|CB667303
EST:     TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAC                         GATTTTACCTCCTTGC
genomic: TGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGC

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: 41 (upstream exon), 73 (downstream exon)
Score: 8

TATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCGAGCTATTGGCTGTGGGCAGCAGgttagtgtta ... acaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATAAATGGACCCATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatcagcacctcaccatatttttctgttttctgatttctcaaaacaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATAAATGGACCCATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGC
                              ttctgat  putative branch site (score: 8)
                 atatttttctgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgcagtgaccaagttaattgattggttttctggaaattcatacacaatcagcacctcaccatatttttctgttttctgatttctcaaaacaattccagGATTTTACCTCCTTGCTAAGGTAGAAGAGGCCGCAGATAAACCTATATATAAATGGACCCATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - -ttgattg
- - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - - cagcacc