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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattttacaagagcaatgtttgctgttacactaatgcctcttggaaggtgacatatttcctattttcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G436835_T02 (Zea mays), 3'ss of exon 9
gtgagcattttacaagagcaatgtttgct---gttacactaatg--cctcttggaaggtgacatat--ttcctattttcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA
||||||  ||||||| |||||  ||||||   || |||  | ||  | | ||  |||   |  | |  ||  | ||| ||  | |||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||| |||||||||
gtgagctgtttacaaaagcaagatttgcttgtgtaacaggactgggcttttttaaagaacaggtttcgtttttttttccatttacagCACAGCAACGAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCCACAAACCCAAATATAAGAACTTCAATGGGGTCTGCTGCATATGCTCCTGAGAGA

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 8
gtgagcatt--ttacaagagcaatgtttgct---gttacactaatgcctcttggaaggtgacatatttcctattttcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA
||||    |  ||||||  ||||  ||||||    | |||  ||||    ||   |    |    |||| | ||| |   | |||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||| |||||||||
gtgaatgatatttacaaacgcaagatttgcttgtatgacaggaatgtgctttttgaaagaatgggtttcttttttccgtttacagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGA

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0225g00220.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------gtgagcattttacaagagcaatgtttgctgttacactaatgcctcttggaaggtgacatatttcctattttcacct-gcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA
                                           |  |  ||    || | |||| ||    |||| || |     |     |  ||||  ||    |  ||| |  | ||||||| ||||||||||||||||||||| ||||||| || || |||||||| || || |||||  |||| |||||||| ||||||||||||||||||||||  
gtatatttctttaggtcttggctactgatctctatctagtctagcacccttggtcagggtaatgcttagcattac-ctgagttgacccatgaattgacccatgagttgatttaattttgcagCACTGCAACAAATGTTGAAATTGAATTGCCTGTACCATCTGATGCTACCAATCCAAATATTCGAACATCAATGGGATCTGCTGCATATGCACCTGAGAAT

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|29672963|gb|CB669238.1|CB669238
EST:     AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAG                         CACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
genomic: AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAGgtgagcattt ... tcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
EST: gi|58589259|gb|CF987567.1|CF987567
EST:     AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAG                         CACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
genomic: AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAGgtgagcattt ... tcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
EST: gi|163929166|gb|EG712667.1|EG712667
EST:     AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAG                         CACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
genomic: AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAGgtgagcattt ... tcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
EST: gi|27554506|gb|CA998406.1|CA998406
EST:     AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAG                         CACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
genomic: AGCCGAATAGAACTTATGGTGAAAGCAAGAAGTCAGTTTAAGGAAAGGAGgtgagcattt ... tcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
EST: gi|163927958|gb|EG714266.1|EG714266
EST:     AGTCAGTTTAAGGAAAGGAG                         CACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA
genomic: AGTCAGTTTAAGGAAAGGAGgtgagcattt ... tcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttacactaatgcctcttggaaggtgacatatttcctattttcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA
        cactaat  putative branch site (score: 2)
                                   tttcctattttcacct  putative PPT
                                atatttcctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcattttacaagagcaatgtttgctgttacactaatgcctcttggaaggtgacatatttcctattttcacctgcagCACAGCAACAAATGTTGAAATTGAAGTGCCTGTTCCTTCAGATGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC