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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttattactacaatttgctcctttttttttgcttgatgcgatttataaccctttctcattgcag

Basic information

species Oryza sativa
transcript LOC_Os08g26870.2
intron # 4
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 4
lower sequence: GRMZM2G377595_T01 (Zea mays), 5'ss of exon 4
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttatta------ctacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcag
|||| ||||||||||| ||||||||| | | |||||| |||||||||||||||||  ||| | || | |      |||  ||||  | || | | || |||||||||   | ||||  || | ||    ||  ||
TGGAGATGCCAAGCGTTCTTCTGATGCCAGTTATTCGTAATGTCCACATTgtaattccttctattgtcatcaattctattatttcatactatctgttctgcttgatgtagtctatataacacctttctgttatag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G053531_T02 (Zea mays), 5'ss of exon 4
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttatta------ctacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcag
|||| ||||||||||| ||||||||||| |||||||| |||||||||||||||||  ||| | |||| |      |||   |||  | || | | || |||||||||   | ||||  || | ||    ||  ||
TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattccttctattatcatcaattctattgtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 3
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttat------tactacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcag
|||| |||||||| |||||||||||||| |||||||| |||||||||||||||||||||| | || |      ||||||  |||| | || |   || || || |||   | ||||  || | ||    ||  ||
TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatcttctattgtcattaatactactgtttggtactgtccattctgtttcatgtagtctatataacgcctttatgttatag

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G146355_T01 (Zea mays), 5'ss of exon 6
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttattacta-------caatttgctcctttttttttgcttgatgcgatttata--accctttctcattgcag---------------
|||| |||||||||||  |||||||||| |||||||  |||||||||||||||||  ||| | || | |  |          ||    |  | | || |||||||||   | ||||  || | || |  ||  ||               
TGGAGATGCCAAGCGTTATTCTGATGGCAGCTATTCATAATGTCCACATTgtaattccttctattgtcatcaattatattgtttcatactatctgttctgcttgatgtagtctatataacacctttttgttataggcatgaccgaccata

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G148892_T01 (Zea mays), 5'ss of exon 3
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttatta------ctacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcag
|||| ||||||||||| ||||||||||| |||||||| |||||||||| ||||||  ||| | |  | |      |||   |||  | || | | || |||||||||   | ||||  || | ||    ||  ||
TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACAATgtaattccttctatagtcatcaattctattgtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatag

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:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29660675|gb|CB656950.1|CB656950
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29659550|gb|CB655825.1|CB655825
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|27920437|gb|CB096245.1|CB096245
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|109974602|gb|DT806998.1|DT806998
EST:     GTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: GTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29629367|gb|CB634378.1|CB634378
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29663843|gb|CB660118.1|CB660118
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|3767979|gb|AU032006.1|AU032006
EST:     TGGAAATNCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29659488|gb|CB655763.1|CB655763
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29670738|gb|CB667013.1|CB667013
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29675966|gb|CB672241.1|CB672241
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29671385|gb|CB667660.1|CB667660
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|84117164|gb|CD150931.1|CD150931
EST:     GTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: GTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29659844|gb|CB656119.1|CB656119
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29669212|gb|CB665487.1|CB665487
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|58687907|gb|CK076594.1|CK076594
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29664873|gb|CB661148.1|CB661148
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|218495687|gb|FG969804.1|FG969804
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCACGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29657113|gb|CB653388.1|CB653388
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29678163|gb|CB674438.1|CB674438
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29658491|gb|CB654766.1|CB654766
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|58692668|gb|CK081355.1|CK081355
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29629366|gb|CB634377.1|CB634377
EST:     TGGAAATGCGGAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29668681|gb|CB664956.1|CB664956
EST:     TGGAAATGCCAAGCGTACTTTTGATGGCTGCTATTCGGAATGTCCCCATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29660157|gb|CB656432.1|CB656432
EST:     TGGAAATGCCAAGCGTACTTTTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29669928|gb|CB666203.1|CB666203
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29672180|gb|CB668455.1|CB668455
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|33683462|gb|CF311701.1|CF311701
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29657533|gb|CB653808.1|CB653808
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|58605333|gb|CK033366.1|CK033366
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|29659233|gb|CB655508.1|CB655508
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttattactacaatttgctcctttttttttgcttgatgcgatttataaccctttctcattgcag

- - - - - - - - - - - - - GCTGCT