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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGTGAAGATGCAGCTGCAGGCGATGTCGGCGGCGTACAAGGCCCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatcactaccattcgcaccaatccttagctactttaattggtcaatccaagagcaaagttcttgttttcagttttctgcattcatctgaaaagactgaaatctgagaccgtagatcaatcaacctgaatttcacccctggcaacacttggattgaatggctttgctgcatatgcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g55510.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G016435_T01 (Zea mays), 5'ss of exon 1
GCCGGTGAAGATGCAGCTGCAGGCGATGTCGGCGGCGTACAAGGCCCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatcactaccattcgcaccaatccttagctactttaattggtcaatccaagagcaaagttcttgttttcagttttctgcattcatctgaaaagactgaaatctgagaccgtagatcaatcaacctgaatttcacccctggcaacacttggattgaatggctttgctgcatatgcgcag
||||| |||||||||    ||||||||||||||||||| || |||||| || ||||||||||||||||||||||||||||||||  | ||||||||||||||    || |        |||  ||   || |  | |   ||  ||  |  || |        ||   ||  |  ||                                                                                                           
GCCGGCGAAGATGCAAGCCCAGGCGATGTCGGCGGCGTCCAGGGCCCTGGATCGCTTCGACGTCCTCGACTGCCGGAGCATCGCGTCCCACATCAAGAAGgt----aaccctcgtggctcgtgccgtcccgtctccaaccta--tgaacc-tcgattgattgggtgggtggctgtag-----------------------------------------------------------------------------------------------------------
















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|88239035|gb|CI240197.1|CI240197
EST:     CTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGCCAGTGCGTGGTGGGCGCCAGC
genomic: CTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|88347654|gb|CI637492.1|CI637492
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|87028422|gb|CI263764.1|CI263764
EST:     ACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|58587033|gb|CF985341.1|CF985341
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGAGCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|88745495|gb|CI768855.1|CI768855
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|86855248|gb|CI265174.1|CI265174
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|86499850|gb|CI142483.1|CI142483
EST:     CGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGCCAGTGCGTGGTGGGCGCCAGC
genomic: CGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|117236843|gb|CT855656.1|CT855656
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|325493446|gb|JG457970.1|JG457970
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|88377097|gb|CI597881.1|CI597881
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|58030677|gb|CX728220.1|CX728220
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|38478856|gb|CF962989.1|CF962989
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
EST: gi|88341102|gb|CI638658.1|CI638658
EST:     ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAG                         GAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC
genomic: ACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGC

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), 55 (downstream exon)
Score: 12

GCCGGTGAAGATGCAGCTGCAGGCGATGTCGGCGGCGTACAAGGCCCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatc ... atatgcgcagGAGTTTGACATGATCCACGGGCCGGGATGGCAGTGCGTGGTGGGCGCCAGCTTCGGCTGCTACTTCACGCACAGCAAGGGAAGCTTCATCTACTTCAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGTGAAGATGCAGCTGCAGGCGATGTCGGCGGCGTACAAGGCCCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCCGCTCACATCAAGAAGgtcggtaatcactaccattcgcaccaatccttagctactttaattggtcaatccaagagcaaagttcttgttttcagttttctgcattcatctgaaaagactgaaatctgagaccgtagatcaatcaacctgaatttcacccctggcaacacttggattgaatggctttgctgcatatgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG