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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaactgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT

Basic information

species Oryza sativa
transcript LOC_Os02g32110.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttc-cacaatagttttaagaaataggtagctcaggatagatcctacctttag---tccctatctattctgaaac-tgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
       ||      ||  | |  | | |||  |      |     ||||| ||    ||  | |  |||  |          | |||||  |  | | | | |     || ||| | ||  |||    |    ||  ||  || ||| ||||  |  | |  |  | | |  || |||||||||||||| |||||  | || || ||||||||||| |  ||||| || ||||||||||| ||||| |||| ||| |||||||||||||| ||||| |
------gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggacc-----atggattccactattaaagatgtacatggatattgtaacatgcactttta-tcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT

upper sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccaca-atagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaactgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
       ||      ||  | |  | | |||  |      |  |  ||||| ||    ||| | |  |||  |          | || ||  |  | | | | ||  |  |  || || |  |  || | |   |||| | | | ||||  |  | |  |  | |  | || ||||||||||| || |||||  | || || ||||||||||| |  ||||| || ||||||||||| |||||||||| ||| |||||||||||||| ||||| |
------gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaaca-tgcactttta-tcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT

upper sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 2
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaac-tgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
         ||   | || |||  | | | || ||  |  |     | | | ||  | | | | || ||  |   ||   |  |||   ||  || | | || | || ||  |   |||||    |||  |  ||      ||| ||||| |  | |  |||| |   | ||  ||||||||| || |||||  | ||||| ||| || | || || ||||| || ||||||||||| ||||||||||  || |||||||||||||| ||||| |
--------gtacaagatt-tttcacatatcac-tgttagttttacttaagtatttgaaccaattat-atgctg--tcttgagaagtaacaaagaa-aagcagtttag-atgtaggatacct---atccaaaagtaacacataacatgcattt-tattcattattttgttcta--gGAAGAGAAGGCAATTGAAAGAGGGATTCTTACACTACTACGGCGTGCTACCTTGGTTCAAACATTTGGACAGAGAAATCATGTGTGCTTGAAAGAGGGCT

upper sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
gtaatgatatattggtttatttgtcttct--tacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaata-ggtagctcaggatagatcctacctttagtcc---ctatctattctgaaactgcatatgcaatggttatatgtcttt----------acagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
||||  |  |     ||  ||||||  |   |||   || |       ||  |    |||   | | ||| | |  |     |  |  |     | ||   ||   ||||    |   ||  ||   |||    ||  |||  || |   | ||  | || |||   | |||   |          |||||||||||||||||||||  | || || ||||  |||||||  |||||||| ||||||||||||||||||||   ||| ||||| |||||||| || || |
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctg-cttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT

upper sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 2
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaactgcatatgcaatggttatatgtctt-tacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
                                                                           | |  |||  |    | |  |   | |   |  ||   |  ||| ||   ||      ||      |  ||  | | | ||  || |  || || |  ||||||||||||||||||| || ||||| || ||||| ||||  ||||| || |||||||| ||||||||||| | |||||||||||||||||| |||||||
-------------------------------------------------------------------------aatgcgaaatcctgcctacatttgaattgaaaaatattcgttgtacttt--atcttggcataactcacatgtgagtgttccatctttgttcgtattgtgtagGAAGAGAAAGCTATTGAACGGGGGATTCTCCCATTACTCCAACGTGCAACCTTGGTTCAGACTTTTGGACAAAGGAACCATGTGTGCTTGAATGAGGGTT

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|58604092|gb|CK014620.1|CK014620
EST:     ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAG                         GAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA
genomic: ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAGgtaatgatat ... gtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA
EST: gi|218490368|gb|FG951159.1|FG951159
EST:     ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAG                         GAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA
genomic: ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAGgtaatgatat ... gtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA
EST: gi|218491911|gb|FG966985.1|FG966985
EST:     ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAG                         GAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA
genomic: ATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAGgtaatgatat ... gtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACA

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), 75 (downstream exon)
Score: 41

CCAGTTTCTTTCAAGAAAATGGCCATTCTGGAATAGAACTGATGGAGCAGATCATTTCTTTGTTGTTCCACATGATTTTGGGGCATGCTTTCACTATCAGgtaatgatat ... gtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttagtccctatctattctgaaactgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
                                            tgtcttt  CT-rich tract
          tatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaactgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG