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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattctctcttcacgtgcagttcaagttaactacaaaggctatttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 25
gtaaattctctcttcacg------tgcagttcaagttaactacaaaggcta----------tttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT
||||| | ||||  | |       |||||   |  ||  | |   ||   |          | ||||| |||||  |||||| |||| ||||||||||| || ||||| ||  ||||||| || |||||||  ||||| || ||||||||| |||| |||||||||||| |||||||||||||| ||||||
gtaaactgtctcccctcacttgtttgcagaatacatttgcaatggagttcagtatgaaggttctcatttctcactataacttcacttgcagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCCACATTCTCGTGTGATAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 9
gtaaattctctcttcacgtg----cagttcaagttaactacaaaggcta------tttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT--------------------------------------------------------
||||| | |||| |||| ||    ||| | |   |  | |   ||   |      | ||||| | |||| |||||| |||| ||||||||||| || ||||| ||  ||||||| || |||||    ||||| || || |||||| |||| |||||||||||| |||||||||||||| ||||||                                                        
gtaaactgtctcctcacttgtctgcagattacacttgcaatggagttcagtatgttctcatttcccaccataacttcacttacagtggcctgttcgagagaattcacctccaatcacacatgctgcattctcgtgtgacagTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCC

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G550865_T01 (Zea mays), 3'ss of exon 10
gtaaattctctcttcacgtg----cagttcaagttaactacaaaggcta------tttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT
||||| | |||| |||| ||    ||| | |   |  | |   ||   |      | ||||| | |||| |||||| |||| ||||||||||| || ||||| ||  ||||||| || |||||    ||||| || || |||||| |||| |||||||||||| |||||||||||||| ||||||
gtaaactgtctcctcacttgtctgcagattacacttgcaatggagttcagtatgttctcatttcccaccataacttcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGTGACAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT

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|29676284|gb|CB672559.1|CB672559
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|27554431|gb|CA998331.1|CA998331
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|29672341|gb|CB668616.1|CB668616
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|58677432|gb|CK066119.1|CK066119
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACG
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACG
EST: gi|58594272|gb|CF992580.1|CF992580
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCT
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCT
EST: gi|29680681|gb|CB676956.1|CB676956
EST:     AACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|163926688|gb|EG713704.1|EG713704
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|58694029|gb|CK082716.1|CK082716
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|218501279|gb|FG957977.1|FG957977
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|218487225|gb|FG954419.1|FG954419
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|29666551|gb|CB662826.1|CB662826
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|29673861|gb|CB670136.1|CB670136
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|58590233|gb|CF988541.1|CF988541
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|325493903|gb|JG458427.1|JG458427
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC
EST: gi|29628403|gb|CB633414.1|CB633414
EST:     AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAG                         TGGCCTGTCCGTGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCGGC
genomic: AGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGC

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: 75 (upstream exon), 75 (downstream exon)
Score: 56

CACACGTGTTCAGTTCCATCAGGATCAATTGCACTTTCTTGTTGTGCATGAGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctc ... ttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttcaagttaactacaaaggctatttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT
                                           ctttactttc  CT-rich tract
                       tatttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattctctcttcacgtgcagttcaagttaactacaaaggctatttcattactcaccttaactttactttcagTGGCCTGTCCGGGAGAACTCTTCTCCAATAACGCATGCCATGTTCTCCTGCGATAGTCAATTGATTTATGCAAGCTTTCTGGATGCCACTGTTTGCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT