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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactgttgattatatccttcatatttttctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g55150.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G178996_T01 (Zea mays), 3'ss of exon 3
ctattatgtcctgaac-catcatctctcttaaccacatg--aaattgatagcgaactgttgattatatccttcatatttttct-cacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG
     | | | |   | ||| |  | || || |   |||     |   |  |  |    |   |||||  || |  ||||| |  |||     |  |||||||||  | ||||||||||||||||||||||| |||||||| |||| |||||| || ||||||||||||||||||||||||||||||||| ||||||||
----caagacgtagcctcatgaaatttcatagcagaatgttggctctttcacatatatatatatatatattttagttttttttatacatgtgtccatttttcagGTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG

upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G36440.1 (Glycine max), 3'ss of exon 16
---ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactgttgattatatccttcatatttttctcacaaac-acctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG
   ||    | || | |  |||  |  || || |||| |  |||   | |     |  ||  || ||||  |  |  | ||   |    | |    | ||| ||| || ||| ||||||| |||||||||||||||||||||||||  || |  || || ||  |||| | ||||||||||||||||||| | || |||
cttctgacttatcattattcat--ttcctattgaccaaaaaaaa--aacattattcatttccttttatcaatagttatgtttatatgttccaatcatcttttagGTTCTGCTATTGGATTCAGATTGGATAGCCTTCTTAAACTCACAGAGACACGTGCCCGGGATAAGAAGATGACTCTCATGCATTATCTTTGTAAG

upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 14
---ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactgttgattatatccttcatatttttctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG-----
   ||    | || | |  |||  |  || || |||| |  ||||   ||   |  |  |  ||||     || ||| ||| |      ||    | ||| ||| || ||| ||||||| |||||||||||||||||||||||||  || |  || |||||  | || | ||||||||| ||||||||| | || |||     
cttctgacttatcattattcat--ttcctattcaccaaaaaaaatcattattcatttcctt-ttatcaatctcttatgtttatattctccaatcatcttttagGTTCTGCTATTGGATTCAGATTGGATAGCCTTCTTAAACTCACAGAGACACGTGCACGGGACAAGAAGATGACTCTTATGCATTATCTTTGTAAGGTACA

upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G58160.1 (Arabidopsis thaliana), 3'ss of exon 10
ctattatgtcctgaaccatcatctctcttaaccacatgaaattgata---gcgaactgttgattatatccttcatatttttctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG-----
                                    ||||||||  |   |  |||| |  ||  |||| || ||  |  ||| | ||  |    || |  |||  | || ||||| |||| |||||| ||  | |  ||||||| ||| |  ||||||||||||||  | |||||||| ||||||||| ||||||||     
-----------------------------gtgagtttgaaattgtaatgtgttaactctgaatcttatcttttatcctgctct-aaaagtagtgtttgtctagGTGCTGCGGTTGGGTTTAAATTGGACAGTTTGCCGAAACTCAGTGAAACACGGGCACGTAATAACCGAATGACTCTGATGCATTATCTATGCAAGGTAAG

upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 14
----ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactgttgattatatccttcatatttttctcacaaacacctgttt-ttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG
     |   |  ||   ||| ||   || |    |   |||   | | || | |||      || || |       |   |  ||| |    ||||||  || ||| || ||| |||||||| |||||||||| || |||||||||| |||||  || || || || || | ||||||||||||| ||||| | || |||
tgtgttggcacctctctaacaattgcctttacctatgccatatgact-attgagaaagaccaataatttgtactgaaaaatggtcata----cctgttcctttagGTTCTGCTATTGGATTTCGATTGGATAGTCTCCTTAAACTCACTGATACACGAGCCCGGAACAACAAGATGACTCTCATGAATTATCTTTGTAAG

upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S13_282V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------------------------------------------------ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactg--ttgattatatccttcatatttt----tctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG
                                                                                            |||||| ||||   | || |  |    | |      ||   || ||| |||     ||   | | ||||| | ||  |    |     |||||  ||     |||| || ||  |||| || |  ||||| ||||||||||| || | ||||| ||| || || || ||||| |||||||||||||| ||||| ||||||
gtttgtcacataacgtcctggaatcttttgaacctacatttagacttttcaagagttctctacagttatatagcagcttcttggttgcctaatattatatcct---ctatgagattctgttattgtgggattctggtagtgaagcagattacatgtttcctttagatcctaacatacttgaaacatgtgaaagacagGCTCTGCCATTGGTTTCAAGTTGGACAGCCTTCTTAAGCTTACTGATACTCGTGCTCGGAACAATAGAATGACTCTCATGCACTATTTGTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcgaactgttgattatatccttcatatttttctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG
                               ttctcac  putative branch site (score: 2)
                                           cctgtttttc  putative PPT
                      ttcatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattatgtcctgaaccatcatctctcttaaccacatgaaattgatagcgaactgttgattatatccttcatatttttctcacaaacacctgtttttcagGGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - -cctgaac
- - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaca