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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcatttagccatttatccaagctgatggaatcaaaactttgtgcttctttccag

Basic information

species Oryza sativa
transcript LOC_Os06g36740.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G161390_T01 (Zea mays), 5'ss of exon 4
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcattta--gccatt---tatccaagctgatgga--atcaaaactttgtgcttctttccag---------------
|||||| ||||||||||  |||| ||||||||||| |||||||| || ||||||||||||||   |||||||   | | ||  |  | | |  | |   ||  | |||    |  |  ||    ||||  |   ||||    |  |  | |   |               
TTTCTAAATCAACGGCAGTGCATTAATGTGTGGCGATTTATCCAAACTATCAATGAgtatgt---cctttttatctctaaagcttatatgttcaactcctacggtcatccggtgcctgagtcagtggatgagtgaaaccagataataatattttgcgatgctttatacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G072435_T01 (Zea mays), 5'ss of exon 3
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcattta--gccatt---tatccaagctgatgga--atcaaaactttgtgcttctttccag---------------
|||||||||||||||||  |||| ||||||||||| |||||||| || ||||| ||||||||   |||||||   | | ||  |  | | |  | |   ||  | |||    |  |  ||   |||||  |   ||||    |  |  | |   |               
TTTCTAGATCAACGGCAGTGCATTAATGTGTGGCGATTTATCCAAACTATCAACGAgtatgt---cctttttatctctaaagcttatatgttcaactcctacggtcatacggtgcctgagtcaatggatgagtgaaaccagataataatattttgtgatgctttatacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G383817_T01 (Zea mays), 5'ss of exon 5
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcattta--gccatt---tatccaagctgatgga--atcaaaactttgtgcttctttccag---------------
|||||||||||||| ||  |||| ||||||||||| |||||||| || ||||| ||||||||   |||||||   | | ||  |  | | |  | |   ||  | |||    |  |  ||    ||||  |   ||||    |  |  | |   |               
TTTCTAGATCAACGACAGTGCATTAATGTGTGGCGATTTATCCAAACTATCAACGAGtatgt---cctttttatctctaaagcttatatgttcaactcctacggtcatacggtgcctgagtcagtggatgagtgaaaccagataataatattttgtgatgctttatacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G467159_T01 (Zea mays), 5'ss of exon 10
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcattta-gccatt----tatccaagctgatgga--atcaaaactttgtgcttctttccag---------------
|||||||||||||||||  |  |||| |||||||| |||||||| || ||||| ||||||||   |||||||   | | ||  |  | | |  | |   || |   ||    || |  ||    ||||  |    |||    |  |  | |   |               
TTTCTAGATCAACGGCAGTGTGTGAACGTGTGGCGATTTATCCAAACTATCAACGAgtatgt---cctttttatctctaaagcttatatgttcaactcctacggtcttacggtacctgagtcagtggatgagtggaaccagataataatattttgcgatgctttatacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G058328_T01 (Zea mays), 5'ss of exon 3
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcattta--gccatt---tatccaagctgatgga--atcaaaactttgtgcttctttccag---------------
||||||||||||| |||  |||| ||||||||||| |||||| | || ||||| ||||||||   |||||||   | | ||  |  | | |  | |   ||  | |||    |  |  ||    ||||  |   ||||    |  |  | |   |               
TTTCTAGATCAACAGCAGTGCATTAATGTGTGGCGATTTATCTAAACTATCAACGAgtatgt---cctttttatctctaaagcttatatgttcaactcctacggtcatacggtgcctgagtcagtggatgagtgaaaccagataatattattttgcgatgctttatacag

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|88963890|gb|CI031223.1|CI031223
EST:     GCATGAATGTGTGGCGGTTTATCCACACCATCAATGA                         GAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
genomic: GCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttcc ... ttctttccagGAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
EST: gi|29657096|gb|CB653371.1|CB653371
EST:     GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGA                         GAGACATGATTTAACAGAAAGCTTANAGGAGCTGCAGTGCAGAACTCTAAT
genomic: GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttcc ... ttctttccagGAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
EST: gi|87004289|gb|CI296831.1|CI296831
EST:     GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGA                         GAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
genomic: GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttcc ... ttctttccagGAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
EST: gi|86256344|gb|CI012634.1|CI012634
EST:     GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGA                         GAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT
genomic: GATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttcc ... ttctttccagGAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAAT

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: 53 (upstream exon), 65 (downstream exon)
Score: 9

TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttcc ... ttctttccagGAGACATGATTTAACAGAAAGCTTAAAGGAGCTGCAGTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTAGATCAACGGCAAAGCATGAATGTGTGGCGGTTTATCCACACAATCAATGAgtatgtttccctttttgctttttaaattcttgtatggagcatttagccatttatccaagctgatggaatcaaaactttgtgcttctttccag

- - - - - - - GCAAAG