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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttctgtccaaattaatacagtgaagtactgcatatatatgcttgttgtaatagcttgtaatttctagtcttgttaacttaacatgtttcattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTC

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 10
agttctgtccaaattaatacagtgaagtactgcatatatatgcttg-ttgtaatagcttgt-aatttctagtcttgttaactt--aacatgtttcattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTC
     |    |   || |  | | || |  | |  ||   |  ||  || ||  | |   |  |||   | ||||  ||   |  ||  | ||| || ||||||||  ||||||||||||||||||| |||||||| || || |||||||   ||||||||||||| ||||| || |||||||||||| | || ||||| || |
---ggtaaagagggtattggaataaaat-ttactcatggttaattaattatatcaacagattgattgaaaatctttatattgtcaaatctcttttatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC
















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|29658916|gb|CB655191.1|CB655191
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58683974|gb|CK072661.1|CK072661
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAAC
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAAC
EST: gi|58693179|gb|CK081866.1|CK081866
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|29641703|gb|CB646710.1|CB646710
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|38476835|gb|CF960968.1|CF960968
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|25806838|gb|CA762799.1|CA762799
EST:     CCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: CCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58682290|gb|CK070977.1|CK070977
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|86251810|gb|CI019002.1|CI019002
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87041657|gb|CI196279.1|CI196279
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87017349|gb|CI301385.1|CI301385
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|86415586|gb|CI029597.1|CI029597
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|29642127|gb|CB647134.1|CB647134
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87041898|gb|CI196520.1|CI196520
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87038212|gb|CI192834.1|CI192834
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58687550|gb|CK076237.1|CK076237
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87036423|gb|CI191045.1|CI191045
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87041468|gb|CI196090.1|CI196090
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58663458|gb|CK052144.1|CK052144
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|29667131|gb|CB663406.1|CB663406
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58685311|gb|CK073998.1|CK073998
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|29621783|gb|CB626794.1|CB626794
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|58668351|gb|CK057037.1|CK057037
EST:     TTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|10794822|gb|AU108788.1|AU108788
EST:     TTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|87039324|gb|CI193946.1|CI193946
EST:     TGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|86899096|gb|CI296244.1|CI296244
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|88957286|gb|CI095262.1|CI095262
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATATACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|86414361|gb|CI068764.1|CI068764
EST:     CGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: CGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|88974279|gb|CI019952.1|CI019952
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|8857541|gb|AU094859.1|AU094859
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|33656227|gb|CF278841.1|CF278841
EST:     AGCTGAGGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: AGCTGAGG-AGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
EST: gi|29621782|gb|CB626793.1|CB626793
EST:     TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG                         GTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG
genomic: TAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttata ... cattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtaatagcttgtaatttctagtcttgttaacttaacatgtttcattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTC
                                          tttcattttct  CT-rich tract
           ttgtaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttctgtccaaattaatacagtgaagtactgcatatatatgcttgttgtaatagcttgtaatttctagtcttgttaacttaacatgtttcattttctagGTGCTGGAGAAGATAAACAACCCGCATTATCTCTACCGCATGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - -tactgca
- - - - - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatgt