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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaatatgatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg...

Basic information

species Oryza sativa
transcript LOC_Os03g22880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G110233_T01 (Zea mays), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaat-----atgatgcatttttttt---tgttgtggac---atgcatgattgttctattgattcaccacacaatggtgtttgg---------------------------------------------------------
|||||||||||||||| || ||||| ||||||||||| || || || || ||| |||||||||||||||||||||||||||| |||||||||||||| ||||   ||  | |  | | |||| |    ||||     ||| |  | || || |    ||  | | |   ||  ||      |||  |     |  | ||  || |  |  |                                                         
TGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAGCAATATTTCTGCTGGATACACTTGACAAGGACATCAATTCCTTCTCCATGAGAGTCAGgtactgt--ccttgttcatgttctcatataattgtttatggttaacttcttataagcgtaataggccgtatttatagacagtctgctctgatagaaaactctgataatatgaatatgcaaatattccttattatgattatttattgctttctcaataaaacattgcag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G144995_T01 (Zea mays), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctg--gtttcttcttccgt----gttttgggttaatat-----gatgcatttttttttg------ttgtggacatgcatg----attgttctattgat-tcaccacacaatggtgtttgg--------------
|||||||||||||||| || ||||||||||||||||| ||||| ||||| || |||||||| |||||||||||||||||||| |||||||||||||| |||||||  | || |||| |  |    ||||   || ||| |     || ||||  |     |      ||| ||| ||| |||    | | | |  ||| | | |  |   | || | | |                
TGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGGCAATCTTTCTATTGGATACGCTTGACAAGGACATCAATTCCTTCTCCATGAGAGTCAGgtctgttgcttgttctcctataactgtttattgtcaattttctaagaggcatcataggcagggagctttgaggatatgaatgtgccaatatgcccttggtatgattatttactgttttctcaataaaacactgcag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G11560.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaatatgatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacac--aatggtgtttgg----------------------------
|||| |||||||| ||||| |||||||||||||| ||||| || || |||||  | ||||||||||| ||||| || ||||| |||||||||||||| ||||    | | |||  | |||  |     ||||| |       ||||  |  | |  | |    |  |  ||  |   | | |  | ||   |  | |||                               
TGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAGCAATTTTCCTTCTTGATACACTTGATAAGGATATTAATTCATTCTCCATGAGAGTCAGgtagtttgtgttcaacagtgaat-actctaataagtctataattttcatactctaaatagttttcttcctttaaggaaattattaaactcgaaagagttcaattctctgctattcatcaattgtatgcag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G13770.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgt--------------ctggtttctt------cttccgtgttttg--ggttaatatgatgcatttttttttg------ttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg
||||||| ||||| ||||| |||||||||||||| ||||| |||||||||||  | |||||||||||||||||  | ||||| |||||||||||||| ||||               ||| | ||        ||     ||||   ||| || || ||   ||   |||        ||||  ||  | | ||||  | ||    ||  |    ||||  |||   |
TGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAGCTATCTTCCTTCTTGATACACTTGACAAGGATGTTAATTCGTTCTCCATGAGAGTCAGgtagtatgtttcaacattggatgctcaattaattttaaaattttcatggtcaaaataatttgttccctttgagaaaatttgtaaactggaaggattcatgtaacttttggcttgtcaattatgtgcag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G03150.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgt----------------------ctggtttcttcttccgtgttttgggttaatatgatgcatttttttt-----tgttgtggacatgcatgattgttctattgattcaccaca-caatggtgtttgg
||||||| ||||| ||||| || ||||||||||| ||||| |||||||||||  | ||||||||||||||||| || ||||| |||||||||||||| ||||                          ||  || |    | || |   | ||||| ||   |||| |||       ||||| ||  | |  |||  | | |  |||  |     ||||  |||   |
TGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAGCTATCTTCCTTCTTGATACACTTGACAAGGATATTAATTCATTCTCCATGAGAGTCAGgtagtatgtctcaaatttgaatgctcaattaattatagaattttcttattcaatataatttgttttctttgagaacattgtgaactggaagaattcatttctctatttgctttgtcaattatgtgcag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggtta-atatgatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg
||||||||||||| ||||| || || |||||||| ||||| ||||| ||| || | || |||||||| ||||| |||||||| ||  | |||||||| |||| || |||||| |    |||||||  ||  | || |||  || | | ||   ||        ||| || |   |     |||    |   |  ||     
TGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAGCTATTTTCATGCTTGACACACTTGATAAGGATATCAATTCCTTTGCTATGAGAGTCAGgtttgttttcttat----tgttttgcctttcagattatgtcttgtctgttaccgtaagagaaaatggtt-tctgagcagctcatattatgtttttgcag--

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaatatgatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg
||||||||||||| ||||| || || |||||||| ||||| ||||||||| || | || || ||||| ||||| |||||||| ||  |||||||||| |||| || ||| | |||     |||  | ||           | | ||||  | | | | ||   |   ||  || || ||  |    |  |  |       
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattg----------tgtgttttcctcgagaaaattggtagctgaactgtttata-atgttattacag-------

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 5'ss of exon 3
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaatat--gatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg
||||||||||||||||| | || || || ||||| |||||||| ||||||||  | ||||| ||||| || || |||||||| |||||||||||||| |||| || | |     | |||         |  | |  | ||  | || | ||      |||||  || |||  |   ||        |  || ||||  |   
TGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGGCCATCTTCCTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttattaatattcgtccacaaaccttgtctttggtgattgttatcttcaatccgacatatattatttattccttcggagctaatccactggtcctg--

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|218493946|gb|FG949483.1|FG949483
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
EST: gi|27576278|gb|CA998972.1|CA998972
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
EST: gi|396941561|gb|HO188770.1|HO188770
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
EST: gi|58652464|gb|CK041144.1|CK041144
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
EST: gi|58693561|gb|CK082248.1|CK082248
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGA
EST: gi|218493279|gb|FG957984.1|FG957984
EST:     CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
genomic: CTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA
EST: gi|58659606|gb|CK048286.1|CK048286
EST:     TCTTTCTCCATGAGAGTGAG                         GGAATGGTTTGGATGGCATTTTCCTGAGTGGGTCAAAATTGTCAATGACAA
genomic: TCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAA

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: 68 (upstream exon), 66 (downstream exon)
Score: 46

TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttc ... cattttacagGGAATGGTTTGGATGGCATTTTCCTGAGTTGGTCAAAATTGTCAATGACAACTACATCTATGCTAAGCTTGCTGATTATATAAAGGACAAATCTGAGTTG




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