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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaagatctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg...

Basic information

species Oryza sativa
transcript LOC_Os02g57150.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143627_T02 (Zea mays), 5'ss of exon 2
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaagatctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaa-attgcaagtg-
 |||||||| ||||| |||||||||||||||||||||||||| |||||||| || |||||||||||||| |||||||| |||||||| ||||| || ||||||  ||       | || ||   |  |||  | | | || |  ||||  |   |||    | || |   |  |  |   || ||  |   |  |||     
GAAGGAGCTGCGCTCGTACGAGAAGGAGGTGGAGAAGGAGGCTGCCAAGACCGCCGACATGAAGGAGAAGGGCGCCGATCCCTACGACCTCAAACAGCAGgtgctgacaggtcctttgattctcagagcattcttctatcactactttttt--tctgttactgaactcacccactctgccctagtgattgcaaagcatacta

upper sequence: LOC_Os02g57150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA12G34820.1 (Glycine max), 5'ss of exon 2
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaagatctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg
 |||||||| |  || || |||||||| || ||||  || || ||||| || ||||| |||||||| ||||| ||||| ||||| |||||||||||||||||     | ||||   | |||  |||  |    ||||  |      |  || |  | | | |   | |         ||| ||  ||             
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgt-----atatctccattctt-taatcactgtgcttt--caggttatctcttatttacttttctctgttcaaaacaaattttgacag-------------

upper sequence: LOC_Os02g57150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaag-----atctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg---------------------------
 || ||||| | ||| || ||||| || || ||||  || ||||| ||||||||||| |||||||| ||||| || || |||||||| || || ||||||||  |||        | | | |   || | | | |         |||  ||||  |   | |  | |  |  || |||  || | |||    || | |     |                            
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaaatg-ctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag

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|29687350|gb|CB683625.1|CB683625
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88586988|gb|CI704711.1|CI704711
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|38468410|gb|CF952541.1|CF952541
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88552750|gb|CI482788.1|CI482788
EST:     TACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: TACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88541694|gb|CI470980.1|CI470980
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88378742|gb|CI681558.1|CI681558
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88335167|gb|CI658174.1|CI658174
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88487783|gb|CI425054.1|CI425054
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88297278|gb|CI545368.1|CI545368
EST:     CTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88541160|gb|CI468412.1|CI468412
EST:     CGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88578844|gb|CI687799.1|CI687799
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTNTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88329844|gb|CI651516.1|CI651516
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88585329|gb|CI702953.1|CI702953
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|117237837|gb|CT861936.1|CT861936
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88505968|gb|CI433474.1|CI433474
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88579760|gb|CI691745.1|CI691745
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|95101340|gb|CI693086.1|CI693086
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|38475684|gb|CF959817.1|CF959817
EST:     CTGCTGAGATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88544850|gb|CI472375.1|CI472375
EST:     GAAGGAGGAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATNTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: GAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88585466|gb|CI703099.1|CI703099
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88531318|gb|CI459787.1|CI459787
EST:     GGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: GGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88266009|gb|CI376911.1|CI376911
EST:     AAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: AAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
EST: gi|88587701|gb|CI704413.1|CI704413
EST:     CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAG                         GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA
genomic: CTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGA

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: 70 (upstream exon), 73 (downstream exon)
Score: 24

CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaaga ... acgcctgcagGAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaagatctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccccc