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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC

Basic information

species Oryza sativa
transcript LOC_Os02g35870.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 8
gtaacgttaactcccctatc-ttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
|||| ||| ||| |   |   ||  ||  | ||||  |    ||| ||  | || | | ||||||||||  ||||  |||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||| ||||| 
gtaatgtttacttctacactgttacaacatgaattcaagcgctagatttga-tagaggcctgcttgaacctgctctattcatatagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
-------gtaacgttaactcccctatcttga--aatttaaatttgacttgtagcttgaagta------aatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
       |||| |||   | |   |   | |  ||  | | ||       ||| ||||||||       | | ||||||||||   |||  |||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| || ||||||||||| || ||||| ||||| 
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
----gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttga-actggctcctttcatac-agGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
    ||    |  ||| |  | | |    ||  ||  ||       ||           | | ||||    | ||   | ||  ||   ||| |||| || ||||||||||||||||  ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || 
gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
gtaacgtta--actcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgt----------ctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
||||    |     |   ||| ||  |||       |  | | |   ||    | | |||           |   ||| || | | |||   |  ||| |||| ||||| |||||||||||||  ||||||||||| || || ||||||||||||||||| ||||| |||||||||||||| || || || || || 
gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttat-tgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G11330.1 (Glycine max), 3'ss of exon 8
----------------------------------gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
                                   ||     ||     |||         |    ||    |||| ||||    |  || | || ||||  | | |  | |  |  ||| |||| || ||||||||||||||||  ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || 
gtaagtcaactagacttctatgtgtgcgcataaaatattagcaaagaggctactcctcttctatgcttcccattgtggctt----tgtatttatgtttgactttgttt-tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G33700.1 (Glycine max), 3'ss of exon 8
gtaacgttaact--cccctatcttgaaat---ttaaatttgact---tgtagcttgaagtaaatgt----ctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
||||    |     |   ||| ||  |||      |||     |   |||   | |  ||   | |     |   |||  | | | |||   |  ||| |||| || || |||||||||||||  ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || || || || || 
gtaattccactggacttgtatttttgaatgagcccaatccctttcaatgttcttcgttgtggctttgtagttatctgattttgtttcttat-tgtagGGATGTTAAATATCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATATTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 3'ss of exon 8
---gtaacgttaactcccctatcttgaaat--ttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttca-----tacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
    |||   |||      | |  | | ||  ||   ||  |  |     |  |  ||  ||  |   | | | |  |  | |||     |  ||||  |  ||||||| |||||| ||||  ||||||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || || ||||| || 
gtaataatcctaatgtgtgtgttgttatatcatttttttgaatattctattctatttatttgggtttctaaccagttttttctcaaaatgtgtagGACGGCCAAGTACCGTGAACCCGAGTTTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G77810.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttca----tacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
||||  |  | |  | |   |  |  || || |||  || ||         || ||   || ||||  | | |  ||  |    | |||||  || |||||||||||||||||||| ||||||||||| ||||| || ||||||||||| || |||||||| || |||||                   
gtaat-tccatttgcttgagtcaagcttaaagtttctctggttttactggttagattattg-ttgagttagTTTATTGAACTGTTTCAGGACAGTAAAGTACCATGAACCTGAGTATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATC------------------

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttca----tacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
||||  |  | |  | |   |  |  || || |||  || ||         || ||   || ||||  | | |  ||  |    | |||||  || |||||||||||||||||||| ||||||||||| ||||| || ||||||||||| || |||||||| || ||||| || || || || || || 
gtaat-tccatttgcttgagtcaagcttaaagtttctctggttttactggttagattattg-ttgagttagtttattgaactgtttcagGACAGTAAAGTACCATGAACCTGAGTATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATCTATGCCATCTCCAAGGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
                                             |    ||  |    || | |     |||   | |  | | |   |     || |  | |  ||   |  |||| | |  |  |||||||| |||||||||||||| || |||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||| || || || |||||||| 
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacattttttt---cctgctcgtct--tctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 8
--------------------gtaacgttaact----cccctatcttgaaatttaaatttgact----tgtagcttgaagtaaatgtctgcttgaactggctcctttca---tacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
                     | | |  |||      || |   |||     |   || ||||    || | ||  |  |  |  ||| ||||   |   || ||      | ||||| ||||||||| ||||||||||| |||||||||||||| ||||| ||||| || ||||| || ||||| || |||||||| || || || ||||| || 
gtaagtcctactagctcttaatgaagagaacagggatccttgatttggttcctgggtt-gactatggtgaatctcaattttcaattcttcttgctttctttctttcttgtctgcagGACTGTGAAGTATCATGAACCTGAATACTGGAAATTTGGAGAGGAGGGGAATAAGTACTTTCGGCATGCAACCGGGCAGATTTATGCCATCTCAAAGGAT

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|58666495|gb|CK055181.1|CK055181
EST:     GTCAGGCCCAGTTCTCGCTGACAA                         GAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
genomic: GTCAGGCCCAGTTCTCGCTGACAAgtaacgttaa ... tttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
EST: gi|163922994|gb|EG712767.1|EG712767
EST:     CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
genomic: CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaacgttaa ... tttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
EST: gi|29682555|gb|CB678830.1|CB678830
EST:     CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
genomic: CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaacgttaa ... tttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
EST: gi|58666808|gb|CK055494.1|CK055494
EST:     CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA
genomic: CCAAGAACGTATATTGGATGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaacgttaa ... tttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
 atttgac  putative branch site (score: 4)
                                         ctcctttcat  putative PPT
                  aagtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT