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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctatcgggtttccttgtaggtttttcttgttgatgcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG

Basic information

species Oryza sativa
transcript LOC_Os11g43590.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G070553_T01 (Zea mays), 3'ss of exon 10
gtaatttctatcgggtttccttgtaggtttttcttgttgatgcgcttactgaaaaaaccattcttcttgt-----tagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG
|||| |  | ||| ||| | || | |||||| |||||| |   | || ||||||||     | |  || |     |||||||||||||| || || ||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||||
gtaagtattgtcgtgttactttattggttttgcttgttaaca-gattgctgaaaaatttgatatctttatactattagATGGTATGGTCAAGGGTCAAAACCCATGGGCATCATCCATCACCTCGAGCAGGTTGCTGCGGAGCTCTTTGTGGAACTAAATGGTATATTGCAGGAGGTG

upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G10310.1 (Glycine max), 3'ss of exon 10
----------------gtaatttctatcgggtttcct----tgtaggttt--ttcttgttgat-gcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG
                || |    | |    ||  |     || || ||   | ||  || || | |     | |  |||  ||   |  | | |||||| |||||| ||| | ||||  |||||    |||||||||||  ||||||||||||| || | | | ||||||||||||||||||||  |||||||||
gtgagctctcatatcagtgaaacttttttatttctccaagatgaagattaaatgctcattcattgtgtaatttaatgaaagtatatgttctttcagATGGCATGGTCAAGAATAAAAATACATGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGGGGTG

upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G28760.1 (Glycine max), 3'ss of exon 8
-----------------gtaatttctatcgggtttcct----tgtaggttt--ttcttgttgat-gcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG
                 || |    | |    ||  |     || || ||   | ||  || || | |     | |  |||  ||  ||  | | |||||| |||||| ||| | ||||  | |||    |||||||||||  ||||||||||||| || | | | ||||||||||||||||||||  |||| ||||
gtgagctctctatatcagtgaaacttttttatttctccaaaatgaagattaaatgctcattcattgtgtaatttaatgaaagtatattttctttcagATGGCATGGTCAAGAATAAAAATACGTGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGAGGTG

upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------gtaatttctatcgggtttccttgtaggtttttcttgttgatgcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG
                                        || ||   |    |     || |   ||   |  |   |        |  | |      | ||  | | ||||| ||||||| ||| | || |   |  |      |||||||||| |||||||||| || |||| | | ||||| |||||||||||||| ||||||||||
gtttgtagagcaaccattcttctggagtttattgtcaaacaactttatttctataatgatgaaaacttacatcttcattagttgattttgatatgtggatttttgtctcagATGATATGGTCAAGAATTAAGAAGAAACGAGGATTTCCATCACCTAGAGCTGGTTGTTGTGGAGTTTTATGTGGAACTAAATGGTATATAGCAGGGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtaggtttttcttgttgatgcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG
                        cgcttac  putative branch site (score: 3)
                                       ccattcttcttgtt  putative PPT
         tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctatcgggtttccttgtaggtttttcttgttgatgcgcttactgaaaaaaccattcttcttgttagATGGTATGGTCGAGAGTGAAAACCCATGGCCATCATCCATCACCTCGAGCTGGTTGCTGCGGAGCTCTCTGTGGCACTAAATGGTATATCGCAGGGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT