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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct...

Basic information

species Oryza sativa
transcript LOC_Os06g04460.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct--
||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || |  |||||||| || ||||||||||||||  |||| | | |||   |  |     |  |  | |||     |   | | |     ||||| || |  | ||  |||| |    ||||  |||  |  
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgt-acatgtgaga-actgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G28170.1 (Glycine max), 5'ss of exon 4
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgta-----tggtgccctatatgtcgtacttctttcatagtgtacagtccgg----aggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct
||||||||||| ||||| || || || |||||||| ||||||||||| || || |||||| ||||||| || |  ||||||||||| || ||||| ||||     |  | | | ||   |  ||   ||||  |  | |  |   |      |   | ||  |  |  |   || ||  || | | | | |||  |          
GTGATGGGAGAGTATGGCTATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCCGgtaatatatactactccatggtttttagagctttttttatttttatggcaatatcaaagcattaacatgtctgtatgcatatcgtagtttctcctctgaa---------

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 4
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatg----tcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct
||||||||||| ||||| || || || |||||||| ||||||||||| || || |||||| ||||||| || |  ||||||||||| || ||||||||||   |   ||| | |    |   |  | |||  || ||   |   |           | || ||    || ||  |  | | || || |   |  || ||  
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgt---atgcatatcatagt-ttctccctctgaaaatactc

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcat-agtgt---acagtccggaggacctt-----ttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct
|||||||| | |||||| |||||||||||||||||||| ||||||||||| || |||||| |  |||||||||  |||||||| ||||| ||||||||||     |  ||| |    ||||      || |||||   | | |    ||| |  |     ||| |     ||   |   |  || | ||| |  |  | |      
GTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAGgtaa---cctttatttccgatactgagggaatcagtgtctgatacttttcaggtctctaatggttccctacacatcaaagcacagaaagatttatacatttta------

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 4
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcatagtgtacagtccggaggaccttttc--tcgg---tttattggatgccgcaatgttttctcgaagtcaaaacct
|||||||||| ||| || || | ||| |||||||| || |||||||| || || ||||||||| |||||||||  ||||||||||| |||||||||||| | |  || | ||     |  |||||        | ||    |    |  || ||  ||     |  | || | |  | ||||  || || |  || | |   
GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttg-accttctactgtttttttcttgttcttattgcaactggacaaattttctcattcaaacttccaatgtaggtag-aatggattttcaatatccaga---

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|218489547|gb|FG966244.1|FG966244
EST:     CATCATCCCTGATGCGGCTGTACGCAGAGCAATGAATGAAATAAATGCAG                         CACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
genomic: CATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
EST: gi|157651811|gb|EX451445.1|EX451445
EST:     GTACGCAGAGCAATGAATGAAATAAATGCAG                         CACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
genomic: GTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
EST: gi|157651801|gb|EX451435.1|EX451435
EST:     GTACGCAGAGCAATGAATGAAATAAATGCAG                         CACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
genomic: GTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
EST: gi|218488749|gb|FG970419.1|FG970419
EST:     CATCATCCCTGATGCGGCTGTACGCAGAGCAATGAATGAAATAAATGCAG                         CACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
genomic: CATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
EST: gi|55410556|gb|CV722932.1|CV722932
EST:     CATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAG                         CACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC
genomic: CATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTC

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), 63 (downstream exon)
Score: 3

GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgcc ... cttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTCTTCTGGTGAAGAAAGCAGAAGCAGAGGCAGAGGCAAAACACCTTTCCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA