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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatgatcccatcttgccccttttgctgcacaatttactggaaggtttttaaattttatagaaaatttcaggcttttgtaaaatttttgcactttaacggtataagttagcttttcatgtaaaatactagtgaacaacttgcctggtgctttcttctgccctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACA

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 6
gtaatgatgatcccatcttgccccttttgctgcacaatttactggaaggtttttaaatttt---atagaaaatttcaggcttttgtaaaatttttgcactttaacggtataagttagcttttcatgtaaaatactagtgaacaacttgcctggtgctttcttctgccctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACA
                                                     |||||| |   ||  | ||||  |   |||  |    ||       |   | |||| |  ||    |  |   |||     || ||||     |      |   |   | |||   |  ||||||||||||||||| ||||||||||| ||||  ||||| | |||||||||||||||||||||||||||  |||| || || |||||||| ||||||||||||
----------------------------------------------------gtaaattatgacatcaataattatataatttcattgctttcaactgttcgtaaggtaaatattgcagtgac---taatgatttaatgaattttctcatctatatatatatatgcttctcttgcagGTTTCTTCAAGGACCTGAAACTGACCGTGGGACAGTAAAGAAGATAAGAGATGCCATAGATAACCAAACAGAAGTTACTGTTCAGCTGATAAATTATACA
















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|29624477|gb|CB629488.1|CB629488
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|2317379|gb|C22433.1|C22433
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|2317377|gb|C22431.1|C22431
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|58593934|gb|CF992242.1|CF992242
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|58592396|gb|CF990704.1|CF990704
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGGCCTGAAACTGATCGTGCAACAGTTAGGAAG
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAG
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAG                         GTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA
genomic: CTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGA

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: 71 (upstream exon), 73 (downstream exon)
Score: 41

ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAAATATTAGGGAGAAACTGCAGgtaatgatga ... ctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtaaaatactagtgaacaacttgcctggtgctttcttctgccctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACA
                               tgctttcttctgccct  CT-rich tract
     aaaatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatgatcccatcttgccccttttgctgcacaatttactggaaggtttttaaattttatagaaaatttcaggcttttgtaaaatttttgcactttaacggtataagttagcttttcatgtaaaatactagtgaacaacttgcctggtgctttcttctgccctttgtgcagGTTTCTTCAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA