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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgagacatcttcctttttatttatttttccaaccaagtgtttgcataactaaagtatgctcatttgatacgtttttgcatccaaacgattaacag

Basic information

species Oryza sativa
transcript LOC_Os05g01760.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01760.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G846339_T01 (Zea mays), 5'ss of exon 13
CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgagacatcttcctttttatttatttttccaaccaagtgtttgcataactaaagtatgctcatttgatacgtttttgcatccaaacgattaacag---------------
|||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||||  |||| |  ||   |||| ||  ||  |      ||   ||||  ||  | || |||| |  |||    | ||||   | |   || |||   |                
CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaag-gagaaacattatgttttcttccttgctttctttaa---tttgactatgtgaactatgattttttctaccattttcctaccatcacaattcgaataccaaaaccttgcag

upper sequence: LOC_Os05g01760.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 13
CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgagacatcttcctttttatttatttttccaaccaagtgtttgcataactaaagt-atgctcatttga-tacgtttttgcatccaaacgattaacag--
|| || || ||||| ||||| ||  |||||||||| ||||||||||| |||||  |||| ||||| |||||||||||     |||| ||      ||    |||  ||    |||  | ||| | |   | |  | ||  | | |||| |  ||||||  ||          |  |   
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgt----tagacctcactagcttacaatatagttagggccacttattttctttgatgatatcattttaaattgagtgtgtttttatatatttgttgggagtatat

upper sequence: LOC_Os05g01760.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 13
CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgagacatcttcctttttatttatttttccaaccaagtgtttgcataactaaagt-atgctcatttga-tacgtttttgcatccaaacgattaacag--
|| || || ||||| ||||| ||  |||||||||| ||||||||||| |||||  |||| ||||| |||||||||||     |||||||      ||    |||  ||  | |||  | ||| | |   | |  | ||  | | ||||  | ||||||  ||    |     |  |   
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgt----tagacatcactagcttacaatatagttagagccacttattttctttgatgatatcattttaaattgagcatgtttttatatatttattgggagtatat

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|88221087|gb|CI221043.1|CI221043
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|86256753|gb|CI061516.1|CI061516
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|89192299|gb|CI049760.1|CI049760
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|88906135|gb|CI375207.1|CI375207
EST:     TGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|88247670|gb|CI247519.1|CI247519
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|86480070|gb|CI122703.1|CI122703
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|88967069|gb|CI392031.1|CI392031
EST:     AGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: AGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|89191356|gb|CI393209.1|CI393209
EST:     TTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|29674708|gb|CB670983.1|CB670983
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|88246448|gb|CI246297.1|CI246297
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|86480080|gb|CI122713.1|CI122713
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
EST: gi|86479999|gb|CI122632.1|CI122632
EST:     TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG                         GGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG
genomic: TTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG

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: 68 (upstream exon), 61 (downstream exon)
Score: 20

CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgaga ... cgattaacagGGCAAGTCAGAGAATGGAAGACCAGCATGGGAAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAGgtaaatgagacatcttcctttttatttatttttccaaccaagtgtttgcataactaaagtatgctcatttgatacgtttttgcatccaaacgattaacag

- - - - - - - - - - - - - - - - - AGTGGA