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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatggattgtatggtagttaatttttgcatgaaacaacagcatttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT

Basic information

species Oryza sativa
transcript LOC_Os07g22720.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11
gtatatggattgtatggtagttaatttttgcatgaaacaacagc------atttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
|||||| |  || ||  ||| |    |  ||| |||| || |        |     |||||| |  || |   ||   ||||||||| ||||| ||||| |||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||| ||||| |||||||
gtatatcg--tgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 15
gtatatggattgtatggtagttaatttttgcatgaaac----aacagcatttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
|||||| |  ||  |  ||| |    |  ||| ||||     ||    |  | ||||||| |   ||  ||| |  ||||||||| ||||| |||||  ||||||| ||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||| |||||||||||||
gtatattg--tgcgtactaggtgtgctacgcaggaaagtagaaatgagaaatatccatgaca-tattggtgttgcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
---gtatatggattgtatggtagttaatttttg-catgaaacaac-agcatttttc-catgagaactt-ttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
     |  |   ||  |  ||  ||| || ||| || |  |   | ||  |||  |  |||| ||||   |  ||  |  || |||||||| ||||| ||  | || ||  ||||||| || ||||| || |||||||| ||||||||||| |||||||||||||| |  ||  | |||||||| |
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
gtatatggattgtatggtagttaatttt---tgcatga--aacaacagcat--ttttccatgagaactt--ttat-gtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
|||  || |||   |  || ||     |   || |||    |    | |||  | ||  |   ||||||  | ||  |  | | | ||||||||||| || ||  | || ||||||||||| || |||||| | || |||||||||||||| || |||||||| || || |  ||| | ||  |||| |
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------gt-atatggattgtatggtagttaatttttgcatgaaacaa--cagcatttttccatgagaacttttatgtggtg-----ttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
             || || || |   |||| |  ||| |||||   |  |      |  | |||||   | |    ||||     |       | | ||||| || ||||| || || || || |||||||| |||||||| ||||| ||||||||||| ||||| |||||||||||  | || ||  | ||  ||||  
attccgtgtttctgtgatttgaagattatgatttttattttttagtttcatttttccttcgttttttactaaatgttttttaactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

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|86477689|gb|CI120322.1|CI120322
EST:     AGTTGGCTCAAAGAGCAAGGGATAACAGTTTGAAACCAGATGATTATGAG                         GGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAA
genomic: AGTTGGCTCAAAGAGCAAGGGATAACAGTTTGAAACCAGATGATTATGAGgtatatggat ... gtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAA
EST: gi|89192614|gb|CI049912.1|CI049912
EST:     GAAACCAGATGATTATGAG                         GGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAA
genomic: GAAACCAGATGATTATGAGgtatatggat ... gtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAA

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: 74 (upstream exon), 65 (downstream exon)
Score: 27

GATGCAGACAAGAAAGGACTTGGTATGATTGCGGAGGAGGTGAAGCAGTTGGCTCAAAGAGCAAGGGATAACAGTTTGAAACCAGATGATTATGAGgtatatggat ... gtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcatgaaacaacagcatttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
                                              tgttttc  CT-rich tract
                                 aacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatggattgtatggtagttaatttttgcatgaaacaacagcatttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC