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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag

Basic information

species Oryza sativa
transcript LOC_Os10g32730.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G027115_T02 (Zea mays), 5'ss of exon 9
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtt-tctca------atacatccccttt---catgttt--agtacttcagtatattagtttattctaaaagacattggtcacag
|||||||||||||||||| |||||||||||||| ||||||| ||||||||| |||||||||||||||||||| ||||| || || || ||||||||  | ||| ||||| |||||      || ||| || |     |||  ||  | |||| |  | || || ||| ||||||| | |||       ||
GGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGATGGTTATGAGCATTGGCTGGAACCCATATTTCGACAATACCGAGAAGACAGTAgtgggtgttctctcacaccacatgcattccatgcagccattcttctactactact-tctactactttgttctaaacgccatccactgtag

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G06330.1 (Glycine max), 5'ss of exon 3
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattg-gtcacag
 || || ||||  ||||||||| | ||| |  ||||| | ||||| ||||| ||||||||||| ||||| ||||||||  | ||||  ||||||||||| || |||||||  |   ||| | ||    ||   || |    | ||  |||  | |||| |  | | | ||  ||   ||
AGTTTATTTTGATTGGGCTGGATTGTCAGCCAGAGGTGTTTTTAAAATGGTGATGAGCATTGGTTGGAATCCTTATTTCAACAACAAAGAGAAGACTATAgtaagtgttttactgcacacctccagatataactact-tgcctgtgaatttttgtattatctatgcctttttgttgtag

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G21470.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag--
 || |||||||| ||||| ||  |  ||| | ||||| | ||||| ||||||||||||||||| ||||| ||||||||  |||||| |||||| ||||||||||||     |||  | |    |   ||   ||  |||| ||||   ||  ||  ||        | || || | |   
AGTGTACTTTGGTTGGGCAGGCTTGGCAAAGAGAGGTGTCTTTAAAATGGTCATGAGCATTGGTTGGAATCCTTATTTCAATAACAAGGAGAAAACTATTgtgagt-----tcataaaaagttcaaacaaaattcttactccagtg-gttgcttctttaactttagcttttgttatatag

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv00s0181g00140.t01 (Vitis vinifera), 5'ss of exon 9
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag---
 ||||| || || ||||||||| | ||||  |  ||| | |  |||||||| ||||||||||||||||| || |||||  | ||||| ||||| ||||| |||||||   ||       |     |  |  ||    |  |   |    |   || |||||||   ||||    |      
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatcccatttacaattttag

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag---
 ||||| || || ||||||||| | ||||  |  ||| | |  |||||||| ||||||||||||||||| || |||||  | ||||| ||||| ||||| |||||||   ||       |     |  |  ||    |  |   |    |   || |||||||   ||||    |      
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag

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|27576586|gb|CA999280.1|CA999280
EST:     AACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: AACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29623339|gb|CB628350.1|CB628350
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|89172764|gb|CI022643.1|CI022643
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|33689645|gb|CF317884.1|CF317884
EST:     TTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|86488009|gb|CI130642.1|CI130642
EST:     TGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29613709|gb|CB618722.1|CB618722
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29631921|gb|CB636930.1|CB636930
EST:     AGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: AGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29671819|gb|CB668094.1|CB668094
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTT
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTT
EST: gi|86500552|gb|CI143185.1|CI143185
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29658983|gb|CB655258.1|CB655258
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29629324|gb|CB634335.1|CB634335
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29671820|gb|CB668095.1|CB668095
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29684882|gb|CB681157.1|CB681157
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAACACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAACTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|86861088|gb|CI326597.1|CI326597
EST:     ACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: ACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29623338|gb|CB628349.1|CB628349
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29625607|gb|CB630618.1|CB630618
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|33680484|gb|CF308723.1|CF308723
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
EST: gi|29629325|gb|CB634336.1|CB634336
EST:     TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATT                         GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG
genomic: TCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgttt ... ttggtcacagGAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA