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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgttctttagggatgattgcttttttccccagtttgatctttaagcttgatatgcattttgtaattaccttattcaatgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 8
tctgtgttctttagggatgattgcttttttcc-ccagtttgatctttaagcttgatatgcattttgtaattaccttattcaa--tgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG
     ||| | ||   ||| |   | |  |   ||| ||| |  ||   || | || | | ||||  | |   || |||  |  |  ||||| |||   | ||| ||||||||||| ||||||||||| |||||||| || ||||||||||||||||||||||| ||||| ||||| |||
-aaaagttgtctat--atgttcattctcctgagccatttttaaattcctgcatcattttccttttacattattctaattataattttaactgcaattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G060977_T01 (Zea mays), 3'ss of exon 8
tctgtgttctttagggatgattgcttttttccccagtttgatctttaagcttgatatg--cattttgtaattaccttattcaa--tgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG
    | ||  | |  | ||     | |||||     | ||| |  |    ||| |     ||||   |  |||| |||||| |  |   | ||||||   | ||| ||||||||||  ||||||||||| |||||||| || ||||| ||||||||||||||||| || || |||||||||
---attttaataaaagttggcca-tattttcattgttctgaaccattcttttgttcccgccattgcctttttacattattctaattttgaatgtaattaaatagAGTCTGTGGACAACATCATGCAAGAGTCACATGAGCTTGATGGTACAACAGTAGTTGTTGATCGTGCGACTCCTAAG
















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|117251528|gb|CT844202.1|CT844202
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|58598133|gb|CK008661.1|CK008661
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|32947891|gb|BP184463.1|BP184463
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|58603513|gb|CK014041.1|CK014041
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGAGTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|58672481|gb|CK061167.1|CK061167
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
EST: gi|116875549|gb|EC366057.1|EC366057
EST:     TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAG                         AATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG
genomic: TGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAG

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: 46 (upstream exon), 53 (downstream exon)
Score: 22

GAACATGGTTCAAAGGGTCATCGTGGAATTGGGTTCATCACTTTTCAGAGTGCAGgtacgtttgc ... aatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcttgatatgcattttgtaattaccttattcaatgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG
   gcttgat  putative branch site (score: 22)
              attttgtaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtgttctttagggatgattgcttttttccccagtttgatctttaagcttgatatgcattttgtaattaccttattcaatgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG

- - tgttctt
- - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa