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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtacagtgcctgtaattgaggcatgttatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT

Basic information

species Oryza sativa
transcript LOC_Os02g56550.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G075336_T02 (Zea mays), 3'ss of exon 1
-------tgtacagtgcctgt-aattgaggcatgttatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT
         |  || || |   |   |||   || | |     | |  |  ||||  | | ||| |||   ||  ||     ||| ||  |||| ||||||  | ||||||||||||| |||||||||||||||||||| || ||||||||||||||||||||||| |||||||| || |||||||| ||||||||||| ||||||||
agtgcttcatgtagcgctttccagccgagatgtggtttccagctttgctgagtaaatt-ttatgtaca---acggctt----atgcacttacttatgccaatactcagGCAAGACCACACTCTTGAAGATTCTTGCGGGAAAGCATATGGTTGGAGGAAGAGATGTGGTCCGTGTCCTCAATGGTTCCGCTTTTCATGATACACAGCT

upper sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 1
tgta-cagtgcctgtaattgaggcatgttatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT
 ||| |  |  | || ||||  || | ||||    ||| |   ||| |   ||  ||    || |     || |    |     | | || |      |||| ||||| ||| |  |||||||||| |||||||| || ||||||||||||||||| ||||| || ||  | | |||||| |||||||| ||||| |||||
-gtaacgcttaccgttattgttgctt-ttatcacgtta-cacgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtttgtc------cagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT

upper sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G44110.2 (Arabidopsis thaliana), 3'ss of exon 1
--tgtacagtgcctgtaattgaggcatgt-tatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT
  |    |    |  |  ||     || | |||  | |||      | | |  ||  ||    |||  |       | |||     |  ||  ||    ||||| || || ||  | |||||||||||||| || |||||||||||||||||||   ||||||| |  || ||| || | || || |||||||| ||| ||||
agtaagtaagatcgatttttcgactatatgtatcatgttaatactcgaatttgat--tgattctgctgagaaggtgattgtcgttgcgcgtttcat-tgacagGGAAAACTACGTTATTGAAGATTCTTGCTGGAAAACATATGGTTGGAGGAAAGAATGTTGTACAAGTGCTTGATCGCTCAGCATTTCATGATACAGAGCT

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|27921110|gb|CB096918.1|CB096918
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCTAACGGATCAG                         GCAAGACCACTCTCTTGAAGAATCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|88396566|gb|CI601049.1|CI601049
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|88727100|gb|CI750755.1|CI750755
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|27548820|gb|CA766802.2|CA766802
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCTAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|44668118|gb|CR281552.1|CR281552
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCTAACGGATCAG                         GCAAGATCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|88733885|gb|CI755321.1|CI755321
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|568460|gb|D39309.1|D39309
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|33690072|gb|CF318311.1|CF318311
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
EST: gi|88717137|gb|CI740647.1|CI740647
EST:     CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAG                         GCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA
genomic: CCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAA

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: 50 (upstream exon), 68 (downstream exon)
Score: 10

CTGCAGTTCGACTACGACGGGCAGCCGCCGCTCTTCGCGCGGTTCAATCTCCGCATCGCCCCCGGCTCACGATGCCTCCTCATCGGCGCGAACGGATCAGgttaggtttt ... caaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT
                       tatataatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtacagtgcctgtaattgaggcatgttatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - gtgcctg
- - - - - - - - - - ggcatgt
- - - - - - - - - - - - - - -tgttctt
- - - - - - - - - - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - atcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtgc