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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG

Basic information

species Oryza sativa
transcript LOC_Os03g18310.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 18
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcaccta-ttgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
|| | |   | |||| ||| | |||  ||||  |   ||   ||| | |||||  || || ||  | ||  |     || | ||||  | | || ||| ||| |||| |||||||||| || ||||| |||||||| ||||||||||||||||| |||||| ||||||||
gtcagtattgcctat-tgatactattgcatg--gctcta---tacatgattcagttacttatatgtgttgcc-----acctaatctgaaaattcctctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 20
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
               ||  |   || || |        | ||||  || ||| |  |  |  |||  | | | || |  |    |  |   |  |     | ||| |||||||||||||||||||| ||||| || || || || || |||||||| ||||||||||||
---------------gtagatgcattacttctt--ttaacattatttagttc-caaacggctacttgt-ttgatgtaaataggttaaattttaataataatgcagGTTAGAACCTGTAATTATTGAACTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 31
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgtt-cagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
               ||  |   ||||| |        | ||||  || ||| |  |     ||| |  | | || |  | |  |  |   |      |  | ||| |||||||||||||||||||||||||| || || || || || |||||||| ||||||||||||
---------------gtagatgcatcacttctt--ttaacattatttagttc-caaaccactact-tgcttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 27
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
                      |||   || |  | | ||||||  || ||| | |  |  |||| |  | | |  |  | |         |  |     | ||||||||||||||||||||| |||||| | || || || || || |||||||| ||||||||||||
-------------------gtatattttat-cttataaatattatttagttc-cttgcttcaact-tgcttgatataaataactcaagttttagtaataatacagATTAGAACCTGTAATTATAGAGCTTAAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 22
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG-
                  | ||| |  | |  | ||||   |||  |  ||  |  |   |   |  |||   |  |||  |  ||||      |     | ||| ||||||||||||||||| |||||||| || || || || || |||||||| |||||||||||| 
-----------------tatattttatcttataaacattatttagctcctttcctcaacttgtttgatataaata-actcaagttttag-----taataatacaggTTAGAACCTGTAATTATAGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAGG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 21
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
                      |||   || |  | | ||||||  || ||| | |  |  |||| |  | | |  |  | |         |  |     | ||||||||||||||||||||| |||||||| || || || || || |||||||| ||||||||||||
-------------------gtatattttat-cttataaatattatttagttc-cttgcttcaact-tgctagatataaataactcaagttttagtaataatacagATTAGAACCTGTAATTATAGAGCTTGAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgtt-cagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
            | ||  |  |  |   |   |||   || |  |  || | |  |||| |  | |  |  | |  | ||    |  ||  ||| |  |  | |||  | || |||||||| ||||||||||||||||| || || || ||||| || ||||||||||||
-----------gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttcca--actgattta-ttagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG

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|25044722|gb|AJ420705.1|AJ420705
EST:     CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG                         ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
genomic: CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAGgttaattcag ... ctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
EST: gi|86436870|gb|CI118592.1|CI118592
EST:     CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG                         ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
genomic: CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAGgttaattcag ... ctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
EST: gi|58672416|gb|CK061102.1|CK061102
EST:     CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG                         ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
genomic: CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAGgttaattcag ... ctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
EST: gi|88269203|gb|CI380501.1|CI380501
EST:     CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG                         ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT
genomic: CTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAGgttaattcag ... ctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGT

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: 69 (upstream exon), 64 (downstream exon)
Score: 22

ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAGgttaattcag ... ctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
       ttgtaac  putative branch site (score: 22)
                                         tcttctctgttc  putative PPT
     tattgtaactattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT