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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcaccttccaattcgctattaaccatatagtatcagcatctgttgattagcctaagtccatgtcaacatttcatatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGCTATCATGTGCAATGCATAAAGCAGTGGCTTTCTAGGAAGAACACCTGCC

Basic information

species Oryza sativa
transcript LOC_Os05g47670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g47670.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G061663_T02 (Zea mays), 3'ss of exon 3
------------------gtaagcgcaccttccaattcgctattaaccatatagtatcagcatctgttgattagcctaagtccat-gtcaacatttcatatctc-agGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGCTATCATGTGCAATGCATAAAGCAGTGGCTTTCTAGGAAGAACACCTGCC
                       | |||   |          | |  ||  |    || ||| ||| |    |    |  |  || |    |||||| | | || ||||||| || |||| | | |||||||| |||| ||||| |||||||||||||||||| ||||| ||||||||||||||||||||| |||||||| | || |
gtatgtcccttctctttctccttcccactcacaggcctcacttcatgcacttctgctcggcacctgatacacatgtgacatgtatcggttccatttcctttttccagGAAGAGTTCGAAGTACACGAGGAAACTGGGAAGCTGAGCTGTGGCCACAGCTATCACGTGCACTGCATAAAGCAGTGGCTTTCTCGGAAGAACGCTTGTC
















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|27545871|gb|CA764117.2|CA764117
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|38474313|gb|CF958445.1|CF958445
EST:     ACCCCAAGCATTTCGCAACAGAAGTAGAAAGGAATCGCAGTATTCGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|38471401|gb|CF955532.1|CF955532
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|29662570|gb|CB658845.1|CB658845
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|87026428|gb|CI252382.1|CI252382
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|88226530|gb|CI226446.1|CI226446
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|86494294|gb|CI136927.1|CI136927
EST:     ACCCCCAGCATTTTGCAACAGAAGTAGAAAGGAATTCCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACCAGGGAGGCTGATCTGTGGCCACAG
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAAC-AGGGAGGCTGATCTGTGGCCACAG
EST: gi|29659759|gb|CB656034.1|CB656034
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
EST: gi|27545904|gb|CA764245.2|CA764245
EST:     ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAG                         GAGGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC
genomic: ACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGC

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: 71 (upstream exon), 47 (downstream exon)
Score: 31

TGACGATGAAATCGCTCGCAGCCTTAGGATGGTCAAGTATTCAGCATTCAACCCCAAGCATTTTGCAACAGAAGTAGAAAGGAATTGCAGTATTTGTCAGgtaagcgcac ... catatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGCTATCATGTGCAATGCATAAAGCAGTGGCTTTCTAGGAAGAACACCTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtatcagcatctgttgattagcctaagtccatgtcaacatttcatatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGCTATCATGTGCAATGCATAAAGCAGTGGCTTTCTAGGAAGAACACCTGCC
              tgttgat  putative branch site (score: 31)
                                         atttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgcaccttccaattcgctattaaccatatagtatcagcatctgttgattagcctaagtccatgtcaacatttcatatctcagGAAGAATTTGAAGCAAATGAGGAAACAGGGAGGCTGATCTGTGGCCACAGCTATCATGTGCAATGCATAAAGCAGTGGCTTTCTAGGAAGAACACCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC