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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcgacag

Basic information

species Oryza sativa
transcript LOC_Os05g05160.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G017351_T01 (Zea mays), 5'ss of exon 7
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcg--acag
|||||||  |||||||||| ||||||||||||||||| |||||||||||||||||||| || | | ||||||||||||| |||||||||||||| ||| ||| ||||||   | || |||   |              | ||| ||    | ||  | |  |  | || |||     || ||  ||||| |  |||  |||||    ||||
CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatcactcttgtttctgtcc------------tcaactgacaacagtttgacccacgatagagtat----ctgttttctgactgtaaacttgtgtattataacag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G089484_T01 (Zea mays), 5'ss of exon 8
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcgacag
||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| |||| | ||||||||||||| |||||||| ||||| ||  ||| ||||    || | | |   |||| | || | || |||||  |||   | |  |||  ||  |||  |   |   ||||| |  |||    | |||| |        
CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagat-caaatgtcactcc-ttttctctgccttgaattaagtgataacaatcttaggcccgattgtctg-gtttctgattatctacttgtgaatattatgatag---

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 8
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttat-tttatatgacatggattaaccgatggaacttg-tagctccagttgaatat-atacttgattcttgactat-ctacta--------ttgtatcgacag
| || ||||| || || || || || || ||||| || || || || |  || ||  |||| |  |||||||||||||||||||||   ||||||||||||||     |   | |||     | | ||| ||||||    | | | ||     ||| || | || | ||  | | | | |||  | || |  |  | ||||        ||||    ||||
CTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGGAAATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgta-----tccgtcttagcaattatctatttgacatactcttatccattttttttggtatcacctgctgcctgtcaaagttgggtgttaatcaggccactaatgaaattttgtgattacag

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|66923870|gb|CX110718.1|CX110718
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58589741|gb|CF988049.1|CF988049
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58676444|gb|CK065131.1|CK065131
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GGCTTGTGTTGTCTATTCAGATAACCGGGCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58685382|gb|CK074069.1|CK074069
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GGCTTGTGTAGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58665648|gb|CK054334.1|CK054334
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|86898584|gb|CI292404.1|CI292404
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58668494|gb|CK057180.1|CK057180
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|38477994|gb|CF962127.1|CF962127
EST:     TCATTACC-A-                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: TCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58686748|gb|CK075435.1|CK075435
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
EST: gi|58604748|gb|CK015276.1|CK015276
EST:     AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAG                         GCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC
genomic: AAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCAC

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), 73 (downstream exon)
Score: 26

CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatt ... gtatcgacagGCCTTGTGTTGTCTATTCAGATAACCGGCCACAAAGCACAGCCAGTGTCACTGAGGATCTTTCCAGGTGTTTAATCAGAGACAACAATCTAAAATCACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC