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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaattcaagttattcaattggtatattcttcaagtcttaggagagcatatacatat...

Basic information

species Oryza sativa
transcript LOC_Os01g11580.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g11580.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G167718_T02 (Zea mays), 5'ss of exon 4
CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaa--ttcaagttattcaattggtatattcttcaagtcttaggagagcatatacatat-----------------------------------------------------------------------------
         ||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||| ||| |  | |     | || ||  ||||||||  | |||||   ||   || | |   |    |  || ||    |||    |   | ||||  ||                                                                              
---------ATACAGACACAGATAGTTCATCAGCAGATGGTTCTGATGCTGCACAATCGCCCAGAACGTAGCATCTATAGGCCAGgtatattttgc-attaatgcagcaatcatttgcatttaatgtccaacatttttggtaaattcttcaaaactttttttggatctgcaaaccac-tataactaccaaatgcgcatagaaaaaaaattcatgtcctttatggaaccagcttaattagtcccttgcttttttgttttttctag

upper sequence: LOC_Os01g11580.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G400907_T01 (Zea mays), 5'ss of exon 4
CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaattcaagttattcaattggt--atattcttcaagtcttaggagagc-atatacatat
         |||| |||||||||||||||||||||||||| ||||||||||  || |||||||||||||| |||||||| ||||||||| ||  |  | |     | || ||  ||||||||  | |||||  | |  ||  | ||||  |  | |    | || | ||    ||||   | ||   |
---------ATACGGACACAGATAGTTCATCAGCAGATGGTTCTGATGCTGGGCAATCACCCAGAACGTAGCATCTATAAGCCAGgtatattctgc-attaatgcagcaatcatttgcatttaatgtccaa--taactttggtaaattcttcaagaccagttaactttttttggagctgcaaaccact

upper sequence: LOC_Os01g11580.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G167718_T01 (Zea mays), 5'ss of exon 4
CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaa--ttcaagttattcaattggtatattcttcaagtcttaggagagcatatacatat
         ||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||| ||| |  | |     | || ||  ||||||||  | |||||   ||   || | |   |    |  || ||    |||    |   | ||||  || 
---------ATACAGACACAGATAGTTCATCAGCAGATGGTTCTGATGCTGCACAATCGCCCAGAACGTAGCATCTATAGGCCAGgtatattttgc-attaatgcagcaatcatttgcatttaatgtccaacatttttggtaaattcttcaaaactttttttggatctgcaaaccac-tataactac

upper sequence: LOC_Os01g11580.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G400907_T04 (Zea mays), 5'ss of exon 1
---------------CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaattcaagttattcaattggt--atattcttcaagtcttaggagagc-atatacatat
               ||| ||||||||| |||||||||||||||||||||||||| ||||||||||  || |||||||||||||| |||||||| ||||||||| ||  |  | |     | || ||  ||||||||  | |||||  | |  ||  | ||||  |  | |    | || | ||    ||||   | ||   |
ATTTATCATAGGAAACATGTGCAGATACGGACACAGATAGTTCATCAGCAGATGGTTCTGATGCTGGGCAATCACCCAGAACGTAGCATCTATAAGCCAGgtatattctgc-attaatgcagcaatcatttgcatttaatgtccaa--taactttggtaaattcttcaagaccagttaactttttttggagctgcaaaccact

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|27577799|gb|CB000494.1|CB000494
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|89166471|gb|CI103757.1|CI103757
EST:     CACAGTCACCCAGAACGTAACATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: CACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|89166888|gb|CI104174.1|CI104174
EST:     TGCACAGTCACCCAGAACGTAANATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGANATCGTC
genomic: TGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|88228863|gb|CI226714.1|CI226714
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAAGATCTATAGGCCAG                         ATCTAGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|89168898|gb|CI020979.1|CI020979
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAGCATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|29635205|gb|CB640214.1|CB640214
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|29632451|gb|CB637460.1|CB637460
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAG                         ATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTC
EST: gi|58661552|gb|CK050232.1|CK050232
EST:     GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGTCAG                         ATCTTGATGTCCAGCTGGAAAGT-CACCGAC
genomic: GATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGAC

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: 69 (upstream exon), 68 (downstream exon)
Score: 10

CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttag ... ttatctgcagATCTTGATGTCAAGCTGGAAAGTTCACCGACAATTCTGGCATGATATCGTCAGCGAGATTCAATGCTGTCTTGTAAATTTTGGCTATGTAGGAAGTCTAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATATGCAGATACAGACACAGATAGTTCATCAGCAGATGGCTCTGATGCTGCACAGTCACCCAGAACGTAACATCTATAGGCCAGgtatgtttagttagtgggcaatcattctcttgcattttttttccaaattcaagttattcaattggtatattcttcaagtcttaggagagcatatacatat

- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - TGCTGC