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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaatttagttacaagttttcattgatttaatttttaatactatgtaccttttttcag

Basic information

species Oryza sativa
transcript LOC_Os08g26870.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G146355_T01 (Zea mays), 5'ss of exon 5
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcag
| ||| | ||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||   ||||||||| || ||||||||||||| ||| |  | ||  ||  ||   |  | ||    |||   || |||| |||||  |||||   |   |||| | |   |||| ||||
AGTAACTTTCAAGGGAGAAATATTCCAGAGAGTGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGCAGAACTTTACTCCCGATCATTGTTTgtacgta-atcttttagtttgattcggtgaattcagaagtaggaattttttattgacattaatgcatgtctactctctcaattttctcag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G053531_T02 (Zea mays), 5'ss of exon 3
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcag
| ||||| ||||||||||||||||||||| |   |||||||||||||||||||||||||||||||||||||||| | ||||||||| || ||||||||||||| ||| |  | ||  ||  ||   |  | ||    |||   || |||| |||||  |||||   |   |||  | |   |||| ||||
AGTAATTTTCAAGGGAGAAATATTCCAGAGAATACACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGCGGAACTTTACTCCCGATCATTGTTTgtacgta-atcttttagtttgattcggtgaattcagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G377595_T01 (Zea mays), 5'ss of exon 3
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcag
| ||||| ||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||   ||||||||| | |||||||||||||| ||| |  | ||  ||  ||  ||  | ||    |||   || |||| |||||  |||||   |   |||  | |   |||| ||||
AGTAATTTTCAAGGGAGAAATATTCCAGAGAGTGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGCAGAACTTTACTCCTAATCATTGTTTgtacgta-atcttttagtttgattcagtgaattcagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G006468_T04 (Zea mays), 5'ss of exon 3
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaattt---agttacaagttttcattgat-ttaatttttaat-actatgtaccttttttcag
|| |||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| ||| |  | ||  ||  || |   |||||   |||   ||  ||| |||||  |||||   |    ||  | |   |||| ||||
AACAATTCTCAAGGGAGAAATATTCCAGAGAGTGCACCCCAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGCGAAACTTTACTTCCAATCATTGTTTgtacgtaaatcttttagtttgatttgataatttggaagtaggaacctttaattgacattaatgcatgtccaccttctcaattttctcag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G148892_T01 (Zea mays), 5'ss of exon 2
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctag-aaatttagttacaag---ttttcattgat-ttaatttttaa-tactatgtaccttttttcag
| ||||| ||||||||||||||||||||| || ||||| |||||| ||||||||||||||||||||||||||||   ||||||||| |  |||||||||||||  || |  | ||  ||  || | |  |||||||    | |   |||| |||||  |||||   |   |||  | |   |||| ||||
AGTAATTTTCAAGGGAGAAATATTCCAGAGAGTGCACCGCAACCTACTATTGTTTTGAGGATTGAAGATGGAAGCAGAACTTTACTCCTGATCATTGTTTgtacata-atcttttagtttgatttggtgaatttagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcag

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|29659232|gb|CB655507.1|CB655507
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58687907|gb|CK076594.1|CK076594
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|218495687|gb|FG969804.1|FG969804
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58692668|gb|CK081355.1|CK081355
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29629366|gb|CB634377.1|CB634377
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCGGAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|33683462|gb|CF311701.1|CF311701
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58605333|gb|CK033366.1|CK033366
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAATTCTCAAGGGAGAAATATTCCAGAAAGCGCACCACAACCTGCTATTGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacagttcttcattcaatctagaaatttagttacaagttttcattgatttaatttttaatactatgtaccttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG