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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCTCGTCTTCCACGCCGGCCGCGCCCCCAAGGGCGAGCGCACCAACTGGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccatcccttcctatcttacccttaccttacctgctcatgtatcagattgacccatgtttcagattatatttctatttctcgccatatgtatccc...

Basic information

species Oryza sativa
transcript LOC_Os08g44820.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44820.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G125777_T02 (Zea mays), 5'ss of exon 1
GACCCTCGTCTTCCACGCCGGCCGCGCCCCCAAGGGCGAGCGCACCAACTGGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCC---CACCACAGgtccccccatcccttcctatcttacc-cttaccttacctgctcatgtatcag--attgacc-catgtttcagattatatttctatttctcgccatatgtatccc
    |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||| |   | ||        ||| |||||    | | || |  |   |||    |||||||| |   ||   ||   ||  ||  | | || ||     || || | || | || | |   ||| | |   
---GCTCGTCTTCCACGCGGGACGCGCCCCCAAGGGCGAACGCACCAACTGGGTCATGCACGAATACCGCCTCGAGGGCGATGACGCCGCAGGGATACCGCAGgtatatctacccgtatcccccttcttgcttaccttgcg-acttgcgtgctagtcatacatcacaagtccgtcatcatttatccagttgtagt-gtatttttt--
















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|29629364|gb|CB634375.1|CB634375
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|58691437|gb|CK080124.1|CK080124
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|29660833|gb|CB657108.1|CB657108
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|58672969|gb|CK061655.1|CK061655
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGC
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGC
EST: gi|29661739|gb|CB658014.1|CB658014
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|29621761|gb|CB626772.1|CB626772
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|117210558|gb|CT863552.1|CT863552
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|29676092|gb|CB672367.1|CB672367
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|29638320|gb|CB643329.1|CB643329
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGAATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|29621891|gb|CB626902.1|CB626902
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|88419397|gb|CI599230.1|CI599230
EST:     GGGTAATGCACGAGTACCGCCTCGACG-C-AAACCACCATCCCACCA-AG                         GATT-ATTC-TCGTGTGC-GTAT
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTAT
EST: gi|29625979|gb|CB630990.1|CB630990
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
EST: gi|58665423|gb|CK054109.1|CK054109
EST:     GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAG                         GATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG
genomic: GGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAG

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: 50 (upstream exon), 75 (downstream exon)
Score: 5

GACCCTCGTCTTCCACGCCGGCCGCGCCCCCAAGGGCGAGCGCACCAACTGGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccat ... atgtgtacagGATTCATTCGTCGTGTGCCGTATCTTCCAGAAAGCCGGCCCAGGTCCACAGAACGGGGCTCAGTACGGAGCTCCTTTTGTTGAGGAGGAGTGGGAGGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCTCGTCTTCCACGCCGGCCGCGCCCCCAAGGGCGAGCGCACCAACTGGGTCATGCACGAGTACCGCCTCGACGGCCAAACCACCATCCCACCACAGgtccccccatcccttcctatcttacccttaccttacctgctcatgtatcagattgacccatgtttcagattatatttctatttctcgccatatgtatccc

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