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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccattaccttatttagaatgtattcttttgttcaaagatattttgctctaatgcagtgctatcagtaatcattattaatcttaatactatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g21914.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 10
-ttcccattaccttatttagaatgtattcttttgttcaaagatattt-tgctctaatgcagtgctatcagtaatcattattaatcttaatactatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG
 |||  |||   | | ||    |  |   | |  || ||   | ||       || |   |||||| ||     || ||||||||| ||| | ||  ||||||||||||||||||||||||| |||||||| ||||||||||| ||||| || |||| 
attctaattgtatcacttcc--ttcagcgtgtcatttaatatttttagcatcttattttggtgctaccaacttgcaatattaatctaaattccattgtgtagGTTGATGATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAT

upper sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 8
-ttcccattaccttatttagaatgtattcttttgttcaaagatattt-tgctctaatgcagtgctatcagtaatcattattaatcttaatactatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG
 |||  |||   | | ||    | ||   | |  || ||   | ||       || |   |||||||||     || ||||||||| ||| | ||  ||||||||||||||||||||||||| |||||||| ||||||||||| ||||| || |||||
attctaattgtatcacttcc--tttagcgtgtcatttaatatttttagcatcttattttggtgctatcaacttgcaatattaatctcaattccattgtgtagGTTGATGATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG
















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|218497501|gb|FG955303.1|FG955303
EST:     GACAGATGGCACCCAAGTTTGGCAAGCTAAACAAATCATTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGACTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|86259754|gb|CI065627.1|CI065627
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|163929298|gb|EG711035.1|EG711035
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|88239119|gb|CI240281.1|CI240281
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|27546018|gb|CA764157.2|CA764157
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|58679583|gb|CK068270.1|CK068270
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|33679512|gb|CF307751.1|CF307751
EST:     GACAGATGGCACCCAATTTTGGCAAGCTAAACAAATCATTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGACTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|86886652|gb|CI312537.1|CI312537
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|88509021|gb|CI436527.1|CI436527
EST:     CAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: CAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|313079574|gb|HO213132.1|HO213132
EST:     TGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: TGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|58663098|gb|CK051784.1|CK051784
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|88257250|gb|CI359638.1|CI359638
EST:     AGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: AGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|44673938|gb|CR287372.1|CR287372
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|89179770|gb|CI044049.1|CI044049
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|8857451|gb|AU094769.1|AU094769
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG
EST: gi|218503197|gb|FG958153.1|FG958153
EST:     GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTG                         GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTACGACAAGAG
genomic: GACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAG

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: 73 (upstream exon), 63 (downstream exon)
Score: 6

GTATCTGAATCCAGAGGCGCAGGTTCTCTTGTCACAGCTGAACCGACAGATGGCACCCAAGTTTGGCAAGTTAAACAAATCGTTAGCTGAACTGgtacgcatga ... tatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctctaatgcagtgctatcagtaatcattattaatcttaatactatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG
                       taatcattattaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccattaccttatttagaatgtattcttttgttcaaagatattttgctctaatgcagtgctatcagtaatcattattaatcttaatactatcatgtagGTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - -cttttgt
- - - - - - - - - - - - - - - - - -caaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - aatgcag