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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT

Basic information

species Oryza sativa
transcript LOC_Os03g07570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 1
-aaaaaaaaaaactgttatactagtaagaatc---atggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
  | |      | | |||| |||  || | |    |  | || ||      |||    |  |   | |  |||     ||| | ||   ||||    || |||||| ||||||||||| |||||||||||||| ||||| || ||| |||| |||||||| ||||||||||| || |||||||||||||| || || ||||| |
ccacaccgtgtagtcttattctataaaaacttgaaacagtgacagaatgacgttggcatgctgtctgtctaaacaatttgc-tattcaattgtg---ttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
-----aaaaaaaaaaactg--ttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
     |||      |||||  || |     |||| |   | |  |||  ||   |       || ||| |   |||    ||   ||| ||| || |  || |  |||| ||||||||||| || |||||||| ||||| | |||||||||||| | | | || || |||   || |  || || || ||  | || || || ||||
gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagagg-----acttctcactgagaaa-accatttttttgtttatgact-ttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G14850.1 (Glycine max), 3'ss of exon 1
aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcat---tttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
   ||||  |  |  |    |  |     |  |      |    | | ||||   |  | ||   ||  || ||   ||   ||    || |  | | || ||||||| || ||||||||||||||||| |||||||| ||||| | ||||| | | ||||| |||   || |  || || || || ||||| ||||| ||||
--gaaaatcatatagtcccttgatgtctctttttcattgatttgtttatttcaagtaattatgccttgcaattgaggtgtgattcaaatt-ttgaatgtatagCTGAATATCGTGGAAGGGAAGATGCAATATCTGTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGGATAGTTACTGTTTCTTGCGGACATT

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatg---tgtttctgtttttcattttaa--aatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
                                                                        |||  |   |  |  |   |||         | || ||  | |    |  |||| |     |||  |   |||| |         ||         || |||||||| ||||||||||| ||||||||||| ||||  ||||||| |||   | | ||| | ||   ||||| |||||| |||||||| ||    |||||| 
gtaggtttagacactctcttgaataatgcaatgcgttacttcattttgtataaatggtgtttcaggtgctgcaaattaggtttctgcaggggtagcctcttgtgggagagagacggtccggctctgatcagagtttatactgatggtagaagcaccattgacgtggcattgcagCTGAATATTGTGGAAGGAAAGATGCAGTACCTGTTTGATGAGAGTGGTCGGCGCTACTTGGACGCCTTCGCAGGCATTGTGACAGTGTCTGTAGGCCATG

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ12384 (Selaginella moellendorffii), 3'ss of exon 1
aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
                                            || || |   ||| |   |||   ||||| || |||  |    |  | | || ||||| || |||||||||||||||||||| ||||| |||||||||| ||| ||||| ||| | |||   || |  || || || || |||||    || ||||
-------------------------------------------gtgagtgtgaatttgtgtctttttgatgga-tggattgatcgc-gggcgtcttgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATT

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ33785 (Selaginella moellendorffii), 3'ss of exon 1
aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
                                            || ||     ||| |    ||   |||||   |  |   |   |  | | || ||||| || |||||||||||||||||||| ||||| |||||||||| ||| ||||| ||| | |||   || |  || || || || |||||    || ||||
-------------------------------------------gtgagtgagaatttgtgtccttttgatgga--tcgatcgatcgcgggcgtcttgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATT

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|58653206|gb|CK041886.1|CK041886
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|88313994|gb|CI599996.1|CI599996
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|117224901|gb|CT845968.1|CT845968
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|29636944|gb|CB641953.1|CB641953
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|58664115|gb|CK052801.1|CK052801
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|58695581|gb|CK084268.1|CK084268
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG
EST: gi|88299416|gb|CI572368.1|CI572368
EST:     AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCG                         CTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGACGAGAATGGGAAG
genomic: AGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAG

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: 58

GCACCGGCCCAGGCCGTACGCCGGGTGGAGCGGCGATGAGATCCTCGCGAAGAGGAAGCAGTTTCTTGGATCGTCTGTGTTCTACTACTACCAGAAGCCGgtacaaaccc ... cattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
                                 tttttttttgtccatt  CT-rich tract
               attttaaaatggaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaaaaaactgttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT

aaaaaaa
- - - - - - - - - - - - - - - catggcg
- - - - - - - - - - - - - - - - - - - - ggcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca