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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG

Basic information

species Oryza sativa
transcript LOC_Os06g02550.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 6
gtgctt--tattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
||| ||  |  | |||||  |||  |||  ||| || ||  | |||     | |   || |  || || |||||| | |        |||||  ||||||||||||||||||| |||||||| || ||||| ||||||||||| |||| ||||| | | |||||||||||||| ||||||
gtgattgttgctttgcaatctgtc-tcattttttataat--tttctgcggcattcttttgagttacttatttttt-tat-------tcagTCCCTGCGAAGGATGAACCATCCAAACATTGTAAAGCTCAAAGAAGTCATAAGAGAGAGTGATACGCTGTTCTTTGTTTTTGAGTACATG

upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
|| || |||      |  || ||     |||| |  |  | | | |||   |   ||     |||||||| || | |   |||   ||||  |  | || ||||| ||||| ||||||||||| || |||||||||||  |||| ||||||||  ||| |||||| ||||| ||||||
gtactgtatctcattagctgaaa--ggttttgtttttttttttttttactgtatgttcgctgatttttttcttttct---cattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG

upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 3
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
        | |  ||   | || |   | |   | || ||  ||||| || ||| |  ||||  ||||   || | | |   |  ||||| ||| ||| ||||||||| || ||||||||||| |||| ||||||| | ||||| |||||||| || | |||||| ||||||||||||
-------gtaaaacagtttatacttctgctc--ttattattgctattttatttc-tgtatatggttttaaatttttt-ctttttgcagTCATTGAGAAAGATGAACCACCCAAACATTGTGAAGCTCAGGGAAGTCTTTAGGGAAAATGATATTTTGTACTTTGTGTTTGAATACATG

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|58674281|gb|CK062967.1|CK062967
EST:     AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG                         TCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
EST: gi|58695956|gb|CK084643.1|CK084643
EST:     AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG                         TCTTTGCGAAGGATGAACCATCCGAACATTGTGAAAC
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAAC
EST: gi|29638208|gb|CB643217.1|CB643217
EST:     AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG                         TCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
EST: gi|29641486|gb|CB646493.1|CB646493
EST:     ATCTCCGTGAAGTGAAG                         TCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
genomic: ATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
EST: gi|58689016|gb|CK077703.1|CK077703
EST:     AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG                         CCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATA
EST: gi|29632166|gb|CB637175.1|CB637175
EST:     AGAAAAATTATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAC                         TCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGT
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGT
EST: gi|58695198|gb|CK083885.1|CK083885
EST:     AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG                         TCTTTGCGAAGGAT
genomic: AGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGAT

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: 57 (upstream exon), 59 (downstream exon)
Score: 91

GTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAGgtgctttatt ... cgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
                    cattaat  putative branch site (score: 91)
     atatctattatacttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG

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