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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag

Basic information

species Oryza sativa
transcript LOC_Os01g16970.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 13
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatg--gcttgccttatgatacag
| | |||||||||||||||||||| |||||||||||||| ||||||  |||||||| |||||||||||| ||||||||||| ||||||||   |  |  |      | | | |||||                       |||||||||||||||  | ||    ||     | ||  | ||    | |  | |||
GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAGgtaggtaactct-----acttgcatgccc-----------------------tttctgtttgcaggttctaaattccaaccctttctgttgtttatgctctcgtgcag

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 13
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag
||| ||||||||||||||||| || |||||||| ||||| ||||||| |||||||| |||||||||||| ||||||||||| ||||||||  |    || |         | | |  |||     | | |  |   |||   ||| | ||    | || | |||     |                        
GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAGgtagtatgtctatctgcatgccctttctggttg---caggttctaaattctaactctttctgt---tgtttacactcgtgcag-----------------------

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G35090.1 (Glycine max), 5'ss of exon 14
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgt---gcttctcc--tttt--------catgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag
| |||||||||||||||| || || ||||||||||||   ||||| ||||| || | |||||||||||| |||||  | ||| | |||||     || ||   ||||         ||||  || |  |    |  ||  | | |||| | ||| ||| ||      | |    | | |||||| | |                   
GAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAGgttatatttttcaaattttaaaaatgatatgctgtcatttcttacaattttggctagattat-tgtctctattcattc-tataatgattaaataaactgtct-----------------

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag
| |||||||||||||||| || || ||||||||||||   ||||| ||||| || | |||||||||||| || ||  | ||| | |||||  |     ||||||    ||        | |  |  ||     |  |    || ||  |     | ||    ||  ||  | | ||   ||| | |  | || |
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgt--tatatgttttcaaattttaaaa---atgacatgcagtcatttcttacaattttggcta-gattattttgtctctattcattctgtaatgcttaaataaactg

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgt---gcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag
||||||||| ||||||||||| || ||||||   ||||  ||||||||||| || | |||||||||||| |||||  | ||| | |||||   |    |  | ||| | | || |  |  ||  || |  | |    |     |        |   | |||| | |||  |||    | ||||      || ||   
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggttta--taataatggtgacacgactgccttgcacctt--taac---tagcttttgaactggtag--

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|38481101|gb|CF965190.1|CF965190
EST:     AATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG                         GTTAGGCTTCGATGCGGGCTGAACAATGAACTTAATGGTGTCGATGAGCCT
genomic: AATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctcc ... tatgatacagGTTAGGCTTCGATGCGGGCTGAACAATGAACTTAATGGTGTCGATGAGCCT
EST: gi|88371457|gb|CI602635.1|CI602635
EST:     AATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG                         GTTAGGCTTCGATGCGGGCTGAACAA
genomic: AATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctcc ... tatgatacagGTTAGGCTTCGATGCGGGCTGAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag

- - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA