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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctggctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag

Basic information

species Oryza sativa
transcript LOC_Os05g43570.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 3
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctggctgcattattttgtagtttctatttctgatttacacgt-atgctttgacatggttgtacaaatttcag
||||||||| ||||||||||||  ||||||||||| ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||| |||||  ||||||| ||| | | | |||||||||| ||| |  || || || |||||||  |  | | |||||||
GTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAGgtaccatgtacggtctttctgcattgtttggcattctctatttctgttttgcttgttatcctctgacatgtgtacatatatttcag

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctggctgcattatt-----ttgtagtttctatttctgatttacacgt--atgctttgacatggttgtacaaatttcag--------------------------
||| |  |||||| ||| ||  |  ||   |  |||||||||||||||||| | |||||||| |||||||||||  | || ||||||  ||| |   ||||   ||||   |     |   ||  | || || ||||| |   |   || | || ||||    ||| | |    |                           
GTGAGAATTTGTAAAGAAAAATCTACTGGAAGCGTATATGCAATGAAAAAGTTAAAGAAATCCGAGATGCTTCGACGAGGGCAGgta--atgcactatctgatagcatctctccaaatcaaagagtttagttgtgattaaattggtaattcattaacatctgcgtaaatacgctaatcctctctttatgcggtaaatatcag

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 5'ss of exon 4
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatg--gtctg-gctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag-------------
||| | ||||| ||||| ||  |  ||    |||| ||||| ||||||||||| |||||||| ||||||||||| |||||||||||||| | |  |   | || ||||| || ||   | ||   ||  | |||| || |  ||       |  || ||     ||||  |              
GTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAGgtaccttctgggtcatttgtgctgcttttttcctttgtgaataaatatgatctataaataaataacaa-gtgatttactgaattgtactcaacaaagcttt

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 5'ss of exon 3
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctggctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag----------------
||| |  | || || |||||  |   || || ||| ||||| ||||||||||| ||||| ||||||||||| || || |||||||||     | ||     | |  | |  | |||    |||| || | ||||  | |||    |||  |      |  ||  || |                 
GTGAGATTATGCAGGGAGAAATCAAGTACGACTGTGTATGCTATGAAAAAGCTGAAGAAGTCTGAGATGCTACGAAGAGGCCAGgtaattcatgtgtatacgtttaagttgtctgtgtgatctaatttttatttg-aagtaccggttgctagaagcatggaacattgaagaagctgtaaagctct

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 5'ss of exon 3
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatg--tatggtctggctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag--------------
||| |  | || ||||||||  |   |   |  || ||||| |||||||| || ||||| |||||||||||||| || ||||||||||  |     | || |   |  |||   |||         | ||   | |  |  |   |||| | | | |     |   |                  
GTGAGGTTGTGCAGAGAGAAAACAAGTTCTACAGTCTATGCCATGAAAAAACTGAAGAAGTCTGAGATGCTTCGAAGAGGCCAGgtactttaatctttgtatttttctatttgcttgatagaatcgtgtccactgtggagat-cactttcaaaagatatcggatgctaggaaaacgggagaaatt

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16108 (Selaginella moellendorffii), 5'ss of exon 3
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctg-gctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag
|| || || || ||||||||  |  |     |||| ||||| |||||||| || |||||||| |||||||| || ||||||||||||  || | || | |   |     ||||     | ||    || | || | |  |                              
GTCCGGCTCTGCAGAGAGAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAGgtatgatctttgctttttaccaacatattcaagtgcttacgattttaatattccag------------------------------

upper sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ08009 (Selaginella moellendorffii), 5'ss of exon 3
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctg-gctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag
|| || || || ||||| ||  |  |     |||| ||||| |||||||| || |||||||| |||||||| || ||||||||||||  || | || | |   |     ||||     | ||    || | || | |  |                              
GTCCGGCTCTGCAGAGAAAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAGgtatgatctttgctttttaccaacatattcaagtgcttacgattttaatattccag------------------------------

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|25799292|gb|CA755253.1|CA755253
EST:     TATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG                         GTTGAGCATGTCANAGCTGANAGAAACCTTCTTGCAGAAGTTGATAGTGCT
genomic: TATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgta ... caaatttcagGTTGAGCATGTCAAAGCTGAAAGAAACCTTCTTGCAGAAGTTGATAGTGCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAGgtaccatgtatggtctggctgcattattttgtagtttctatttctgatttacacgtatgctttgacatggttgtacaaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG