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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_Os08g26870.3
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|109974602|gb|DT806998.1|DT806998
EST:     GTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: GTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|84117164|gb|CD150931.1|CD150931
EST:     GTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: GTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|58687907|gb|CK076594.1|CK076594
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|218495687|gb|FG969804.1|FG969804
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCACGTTGTGAAGGAGATGATTGATAAGATGGGT
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|33683462|gb|CF311701.1|CF311701
EST:     TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT                         GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
genomic: TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatctt ... ctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGT
EST: gi|58605333|gb|CK033366.1|CK033366
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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATTgtaatatcttgttttattactacaatttgctcctttttttttgcttgatgcgatttataaccctttctcattgcag

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