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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccacccatactatacttatgctccatatctgttttgatttttcttagaatgctatgttctgctttgagcatttggtagtacttaacgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG

Basic information

species Oryza sativa
transcript LOC_Os06g07090.1
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 2
gtatccacccatactatacttatgctccatatctgttttgatttttcttagaatgctatgttctgctttgagcatttggtagtacttaacgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
||||||||||   ||  |||||      | |  ||| ||  ||       || || ||||   || ||       |||  | ||||||||| || |||||||||||||||||| |||||||||||||| || |||||||||||||| |||||||| || || || ||||||||||||||||||||  | ||||| |||
gtatccaccctgtctgcactta------acagttgtgtttgtt-------gattgttatgcgttgtttc---tgattgtaattacttaacgtgggcagAGATCTTAACCACTCAAACCAGTTCATTGTTGGTCTTGCACTCTGTGCCCTTGGCAATATATGTTCTGCTGAAATGGCGCGTGATCTTGCTCCTGAAGTG

upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 2
gtatccacccatactatacttatgctccatatctgttttgatttttcttagaatgctatgttctgctttgagcatttggtagtacttaacgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
|||||| |||   ||   ||||       ||||||||  |||  |  |  |  |  | | |  |     ||| ||| | || ||||||||| || |||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||||||||| || || ||||||||||| || |||||| | ||||| |||
gtatccgccctgtctgcgcttaccagttgtatctgtt--gatgctgttatgcgttatttctgatttccagagtattggttattacttaacgtgggcagAGATCTTAACCACTCAAACCAGTTCATTGTTGGGCTTGCGCTCTGTGCCCTTGGCAACATATGTTCTGCTGAAATGGCACGCGATCTGGCTCCTGAAGTG

upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------gtatccacccatactatacttatgctc-catatctgttttgatttttctt-agaatgctatgttctgctttgagcatttggtagtacttaa--cgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
                                                                          ||       | |||  | || || |  |||  ||||| ||    ||    ||||   ||| |       |  |    || |    |||||  | ||  |||||||||||| |||||||||||||   |||| || ||||| ||||||||| | || || ||||| || || |||||||| ||||||||  | || || || 
gtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA

upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtatccacccatactatacttatgctccatatctgttttgatttttcttagaatgctatgttctg--ctttgag--catttggtagta--cttaac--gcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
            || |  |    |   ||  | || | | |    |||||| | ||||    |    ||  |  |     ||| ||  ||| | ||   |  ||| ||   ||   |||||||| || ||| ||||||||| ||||||||||||||| ||||||||| | || || ||||| || || |||||||| ||||||||  | ||||| || 
gtatcctttatggtgttaatttttg--attttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT

upper sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S211_68V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatccacccatactatacttatgctccatat-ctgtt--ttgatttttcttagaatgc-tatgttctgctttgagcatttggtagtacttaacgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
   | | |      || |  |    || ||    ||||  ||   ||  | ||  |  |   | ||   |  |   | | |  | ||  ||    | | ||| ||  | |  ||| | |||||||||||||||||  | || || ||||| ||||||||||||||  | |||||||||||  | |||||  | ||||| |||
-agtgctctggggttacatctcaattcaattcattgttcattagattggcatatcagacgcgtctttaccagtacacgtgtatttgttgttttttctg-cagTGACTTGAGTCACACAAACCAGTTCATTGTGGGATTGGCTCTTTGTGCACTTGGCAACATTTGTACTGCTGAAATGGCAAGGGATCTTGCTCCTGAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttagaatgctatgttctgctttgagcatttggtagtacttaacgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
 gtacttaac  putative branch site 
                                       tacttaa  TA-rich tract