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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaacttttgtatgatctactaatgcaagcctaacctattgtttgtag

Basic information

species Oryza sativa
transcript LOC_Os08g40140.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G124557_T03 (Zea mays), 5'ss of exon 5
ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaact-tttgtatgatctactaatgcaa-gcct--aacctattgtttgtag----------------------------------------------------------------------------------------------------
|  | || || || |||||  | ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||| ||||     | || ||    ||  |  || || |||      | ||| ||| || | ||| | ||  |   | |||||| |                                                                                                      
ATGTCGCCGGACTGCAAAACAAGGATGGATCATTTTCTGGCGATATTTGGGGTGAAGTTGACACTAGgtaaaaacctttt-atatgttgccactttg----gacttcccagcataacaacccatgtgagctattagttcaaagtcttgagtttgttgttttttatttctgtatgtaggttctcgtatattgccttatgtaccttatcattactgcaccgtctgcataagattgatgtgcaaaaagctgtggatttcgttgttag

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G124557_T01 (Zea mays), 5'ss of exon 5
ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaact-tttgtatgatctactaatgcaa-gcct--aacctattgtttgtag-------------
|  | || || || |||||  | ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||| ||||     | || ||    ||  |  || || |||      | ||| ||| || | ||| | ||  |   | |||||| |               
ATGTCGCCGGACTGCAAAACAAGGATGGATCATTTTCTGGCGATATTTGGGGTGAAGTTGACACTAGgtaaaaacctttt-atatgttgccactttg----gacttcccagcataacaacccatgtgagctattagttcaaagtcttgagtttgttgttttttatttctgtatgtag

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 3
---------------------------------ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaact-tttgtatgatctactaatgcaa-gcct--aacctattgtttgtag-------------
                                 |  | || || || |||||  | ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||| ||||     | || ||    ||  |  || || |||      | ||| ||| || | ||| | ||  |   | |||||| |               
TCCAGTTCCTCTTCCTTATCTAAATCACGCCAGATGTCGCCGGACTGCAAAACAAGGATGGATCATTTTCTGGCGATATTTGGGGTGAAGTTGACACTAGgtaaaaacctttt-atatgttgccactttg----gacttcccagcataacaacccatgtgagctattagttcaaagtcttgagtttgttgttttttatttctgtatgtag

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G11710.1 (Glycine max), 5'ss of exon 5
ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaacttttgtatgatctactaatgcaagcctaacctattgtttgtag
||||||   | || ||||||||||||||||| ||||| || ||||| ||||||||||| || ||  ||||   |  | || | ||||    | | || | |  | | |  |      |  |||||  |  |||||      |  ||    |||| | |||
ACATTGTCAGCCTGCAAAATGAAGATGGATCCTTTTCAGGGGATATGTGGGGTGAAGTTGATACGCGgta--tttttcttaagatcc---ttttttgttattgattatgtaagagcttactgtatttttaactaaaatccactgaattatttgtct-tag

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G28630.1 (Glycine max), 5'ss of exon 4
ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgta---------aaatcctttt--gatatc--ccatctctgtgct--ctgaactttcaacacaacttt--tgtatgatcta-ctaatgcaagcctaacctattgtttgtag----------------------------------------------------
| ||||   | || ||||||||||||||||| ||||| || ||||| ||||||||||| || ||  ||||         | || |||||    |||    ||| |  | |||  ||| | ||| |||  || |    || || || |  |  | |    | ||   |  | ||||| |                                                    
ATATTGTCAGCCTGCAAAATGAAGATGGATCCTTTTCAGGGGATATGTGGGGTGAAGTTGATACACGgtatttttcttaagattcttttttattattgatcatgtaagagcttactgtatttttaactaaaatccactgaattatttgtcctaggttctcatatattgctatttgttgtctatcaatattacatcgcttggataaaatcaatgtggagaaggctgtgaag

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|58681560|gb|CK070247.1|CK070247
EST:     AATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAG                         ATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA
genomic: AATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatcct ... ttgtttgtagATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA
EST: gi|33381466|gb|CF196809.1|CF196809
EST:     GGGTGAAGTGGACACTAG                         ATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA
genomic: GGGTGAAGTGGACACTAGgtaaaatcct ... ttgtttgtagATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA
EST: gi|58692470|gb|CK081157.1|CK081157
EST:     AATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAG                         ATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA
genomic: AATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatcct ... ttgtttgtagATTCTCATACATTGCAATATGCACCCTCTCTTTGCTGCATCGGCTGGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTGCTGGGCTTCAAAATGAAGATGGATCATTTTCTGGTGATATTTGGGGTGAAGTGGACACTAGgtaaaatccttttgatatcccatctctgtgctctgaactttcaacacaacttttgtatgatctactaatgcaagcctaacctattgtttgtag

- - - - - - - - -  TGAAGA
- - - - - - - - - -  AAGATG
- - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA