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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g02756.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
gtaagtgcttttacataatatatattttctatttcatgag--tcatttcaagttacatactgtcaacatttggaa----ttcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
||||||||||||||||| ||| | || | | |  ||||||  |||  | || ||   |   || || |  || ||    |||||||| ||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||   ||||||||||||||||
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
gtaagtgc-ttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
|||||  | ||||| || | |||    ||     ||| ||     |||||  ||  || || |||    ||    ||| || ||| ||  | ||||| ||||| ||||| ||||||||||||||||| || || |||||  | ||||| || || ||||| |||||||| ||||| || ||||| 
gtaagcccattttaaattaaataatgatttctcgtcaaga-----ttcaaactaagta-tgacaa----tgatgctctatt-cagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 37
gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatt-tggaattctt---ttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
||||||   |    ||||| | ||| |||     | |||   | || || | | ||    ||   ||| |   |||  |   ||  ||  |  | ||||||||||| ||||||||||| ||||| ||| | |||||||| ||  | ||||| || || |||||||| || ||||||||||| ||||| 
gtaagttactaccaataatttttatcttc-----cgtgaacaacttgaactcagatggaatccttattctattatttctgaattctagGATCCGCATGCATTATGGTCATCCAGATGTCTTTGACAGAGTATTTCATATTACACGTGGTGGTATCAGCAAGGCCTCTCGGGTCATCAATATTAGTGAA

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 35
gtaagtgcttttacataatatatattttctatttcatga---gtcatttcaagttacatactgtcaacatttggaattcttttg-----cagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
|||||| | |||| || |   |     | ||||| |||     |||||| || ||    |          |   |  | |  |      ||| ||  | ||||||||||||||||||||||||||||||||| |||| ||||||||  | ||||| || || |||||||| || || ||||| || ||||| 
gtaagttcattta-attaagcaagcaatttatttgatgtcatatcattttaaatttgggataactggagctgaaatctttaataatggccagGGTTCGTATGCATTATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAA

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
-------------gtaagtgcttttacataatata-tatt-ttctatttcatgagtca---tttcaa--gttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
             |||| |  ||     |||| || |||   | |   | | | | ||   |||| |    | | ||  ||    |  |   ||     ||||| || || ||||||||||| ||||| |||||||||||| | || || |||||||| ||||| || || || ||  | ||       || ||| ||||||| 
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatg----tgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 36
----------------gtaagtgcttttacataatatatattttctattt-catgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
                | | |  |||  |  |    |   |   | | |   ||| ||  ||  |  ||  |    |  ||   | |       | | ||| ||||||||||||||||||||||||||||| || || ||  | || || |||||||||||||| || ||||| || || ||||| |||||| | || || 
ttcttcaatgccgtttggatgcacttcgaattgcagtgcttagaccactgatatgtgt-gttctatattttaactaggtaatcctggttgcatatgtacagGGTAAGAATGCATTATGGCCATCCAGATGTATTCGACAGGGTATTCCACATAACGAGGGGTGGTATCAGTAAAGCGTCACGTGTTATCAATCTTAGCGAA

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
                                    | ||||   ||  | || | |||   |   ||   | || || | ||| || ||||||||||| || |||||||||||||| |||||||| || |||||||| ||||| || || ||||| ||||| || ||||| || || ||||||
-----------------------------------gtaagtctactcttggtaga-acttgtagtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 37
gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
                                    |  |||  |||  | || | |||   |   ||   | || || ||||| || ||||||||||| || |||||||||||||| |||||||| || |||||||| ||||| || || ||||| ||||| || ||||| || || ||||||
-----------------------------------gtacgtctattcttggtaga-acttgtagtgttaacagtttttatgcagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

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|300216075|gb|HO088701.1|HO088701
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|88399969|gb|CI588273.1|CI588273
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|33679231|gb|CF307470.1|CF307470
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|29675246|gb|CB671521.1|CB671521
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT

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), 71 (downstream exon)
Score: 39

TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
                                            ttcttttgc  CT-rich tract
                                          aattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA