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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG

Basic information

species Oryza sativa
transcript LOC_Os01g41870.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 5
acctaatgtctgttgaactcgattgtataggcatcttgta-ttcttgttaacttcacaatcctaagataaggttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
  ||  ||     ||    | |||  |||    | ||||  ||| |||| |  |   |||   |   || ||||||||||     ||| ||   | |||||||||||||||| ||  |||| ||||||||||| ||||| |||||||| ||||| || ||||| || || ||||||||
-tctgctgatctctgctagccattcaatattttttttgtggttcctgttgaagtattaatttcatattatggttgtaagttccataatgattgcccgacagGTTGGAGATTTCGGCCTGGCGCGATGGCAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 5
acctaatgtctgttgaactcgattgtataggcatcttgtattct-tgttaacttcacaatcc---taagataaggttgtaagtct-ttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
      |  ||   || | ||||  ||   |  | || |    |   | || | |    | |   |   | |   |||||| | |  | ||| ||||| ||  ||||||| ||||||||  ||||| | ||||| |||||||| |||| |||||| || || ||||| ||||||||||| ||
-----tttcctagagatcacgatcttaagtgtgtgttttgagatgcatcaaatgcgtgcttcatttctaacagtattgtaattgtgctgaattatgttatgtaagGTTGGCGATTTTGGACTGGCAAGGTGGCAGCCTGATGGAGACACGGGTGTGGAAACTAGAGTGATTGGAACATTTGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42760.2 (Glycine max), 3'ss of exon 8
-------------------acctaatgtctgttgaactcga--ttgtatag---gcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtct-ttcaataat--------gttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
                    | |  ||  | |  | |  |   || |||||     || |   |  |      ||||  |  |  |     || ||| | | |   || ||||||         ||||   ||||||| ||||||||  ||||| | ||||| |||||||||||||  || || || || |||||||||||||| || ||
gtagggttgtgttttgcctgctttgtgcttttgcagccaggagttttatagtttatatatgaaaggcgccactacttatcttttttgcccaaaagttttcacttcattaaataattgtgttaaattcttcaagGTTGGTGATTTTGGACTGGCAAGGTGGCAGCCTGATGGTGACACAGGAGTGGAAACTAGAGTAATTGGAACGTTTGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G02680.1 (Glycine max), 3'ss of exon 5
-------------------acctaatg-tctgttgaactcgattgtatag---gcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtctttcaataat------gttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
                    | |  |  | ||  |    |  || |||||     || |   |  |      ||||  |  |  |   | ||| ||  |  || || ||||||       ||||   ||||||| ||||||||  ||||| | ||||| |||||||||||||  || || || || |||||||||||||| || ||
gtacggttgtgttttgcctgctttgtactttgcagccagcagttttatagtttatatatgaaaggcaccagcacttatctttgtttcaaaaagttttcacttcattaaataattgttaaattcttcaagGTTGGTGATTTTGGACTGGCAAGGTGGCAGCCTGATGGTGACACAGGAGTGGAAACTAGAGTAATTGGAACGTTTGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
----acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtc--tttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
       |||     ||    |||  |  |     || |   ||| |        |||| |  | |    |   ||  | ||||   ||  ||||| |  |  |||||||||||||||||  | ||| ||||||| |||||||| || |||||||| || ||  |||| || ||||| |||||
gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccact---gtttcatatgctt----tttcgtcctgagtcaactttgataatatcat--cagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G55200.1 (Arabidopsis thaliana), 3'ss of exon 5
acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
                        ||||    || || |         |  | |||  |  | | | |    | | | ||| |   |  |  |||  ||||||||||||||||| || ||| ||||||| |||||||| ||  | ||||| |||||| | || || ||||| |||||
------------------------gtatttatattttcttgaaccacaatttacact-tttttatacattcgtttgattctgtttttgtttctctttcagGTTGGAGATTTTGGTTTAGCAAGATGGCAGCCTGATGGAGAGCTAGGTGTAGACACGCGTGTGATAGGAACTTTCGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataag-gttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
| |   ||| |||      | |  |   | | | | |||    || |     |         | |||  | |   |    |||       || | |  |||||||||||||||||  ||||| | ||||| || ||||| |||||||| || || ||  || ||||||||||||| ||
aacctctgtgtgtctg-tgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------acctaatgtctgttgaactcgattgtataggcatcttgtattcttgtta-acttcacaatcctaagata----aggttgtaagt--ctttcaataatgttctgac-agGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
                                                              |    |    |||     |   || |  |||  | | | ||   ||||  ||||   ||   ||  |||    | | |  |  |  ||   | |  || | |||  ||||||| ||||||||  ||||  | ||||| |||||||| |||| |||||| || || ||||||||||||||||| ||
gtatgccagtttcttaatcttatttccattttttcaaagttaaacatatttgaacgtgataaataagacaattgtgatgttattttttcaaggggtatggaatctgtgttttacttggtaaagatagcatatagaaagcttgaccttactcctacttttgctttgattagGTTGGGGATTTTGGCCTGGCTAGGTGGCAGCCTGATGGAGACACGGGTGTGGAAACAAGAGTAATTGGAACATTTGG

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|25798254|gb|CA754215.1|CA754215
EST:     GTGACATGAGACCAAACAACATCCTTGTTACACATGATTATGAGCCACTG                         GTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTT
genomic: GTGACATGAGACCAAACAACATCCTTGTTACACATGATTATGAGCCACTGgtatggtgtg ... gttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaacttcacaatcctaagataaggttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
 tgttaac  putative branch site (score: 2)
                                   tttcaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG

- - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - cttcaca