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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacattttagctaactggtgctgtttacctttacag

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G149751_T02 (Zea mays), 5'ss of exon 2
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacatttta-gctaactggtgctgtt-tacctttacag
|||| || ||||||||||| ||   |||||||||||| ||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||| ||| |||||| | |   ||      |  |  ||||   ||   || |  |||| |||| || |||||  ||| ||      |||| ||| |||||||
GGACTGGAGGAGAGATTGGATTTGACACCTACTTCTCCATGGCCAGGGGCAACGCCACTGTTCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtgagtcctttgcctgc---ta------ccaatggtaa-ttttagtttgagcttttgtatttaatattttttgctgacaaactttgttctacttttacag

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S399_19V6.3 (Physcomitrella patens), 5'ss of exon 2
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacattttagctaactggtgctgttt---acctttacag---------------
|||| ||||||||||||||   |      || ||||| |||||  | |||||    ||    || || |||||||||||||||||||| || ||||||||||||||      ||||  |      |     || ||     || ||    | |   ||  ||||  |||| |    | |||  |  ||   || | | ||                
GGACGGGTGGAGAGATTGGACACGATGTGTATTTCTCAATGGCCCGTGGAAACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgaccaacttcactaatcattcgtcaaccgtttgtcttctaggagactggaatcctcaaattttttgagcgcgggtcttagttgtaacttgtgcatcgtttttgcgcgcag

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S27_81V6.1 (Physcomitrella patens), 5'ss of exon 2
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacatttta-------ttta----atttttatattcaacattttagct----aactggtgctgtt--taccttt-acag--------
|||| ||||| ||||||||         |||||||||||||||  | |||||    ||    || || |||||||||||||||||||| |||||||||||||| ||||  |  |      |||  | | |    ||| | ||  ||       | ||    ||||| | |||  | |   | | |    || | || |||    | ||||| |||         
GGACTGGTGGGGAGATTGGCCATGATGTCTACTTCTCGATGGCCCGTGGAAACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGACACCAACTAgtatgtacaatcttgatccataacgtattttcttgtacaaatgctagcgcctgtgtaggctattttgagatttcatacagtggttggggaagtagttctgacgctgcctttgacatgttcacag

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S33_110V6.2 (Physcomitrella patens), 5'ss of exon 2
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttattt-----------aatttttatattcaacattttagctaactgg--tgctgtttacctttacag------
|||||||||||||||| |||  |      ||||||||||||||| | |||||    |||   ||||| ||||||||||| |||||||| ||||||||||||| |||    ||| |   | ||  |  | |     |     | |||||            | |||| || ||| | | |  |||| | ||   ||   |  ||||  | |       
GGACCGGTGGAGAGATCGGGCACGATGTGTACTTCTCGATGGCTCGCGGAAACAAGACTAAGCCTGCCATGGAGATGACGAAGTGGTTCGACACCAACTAgtgagtg---tgcctttctatagcaccttttctcttctgtgtattattgtgaagtgcaggagttttcatcttccagacta-agctgattgacctgaaatgaacctgaatacttgcag

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ05611 (Selaginella moellendorffii), 5'ss of exon 1
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacattttagctaactggtgctgtttacctttacag
|||| ||||||||  | |  |||  |||||| ||||| ||||| || || |||||||     || |||||||||||||| || ||||| ||||| ||||||||||||  | ||||     |  ||| | ||   |  ||    | |  |  |    || ||   ||                                
GGACTGGTGGAGATGTGGCCTTCGACACCTATTTCTCCATGGCGAGAGGGAATGCCAAGCAACCGGCTATGGAGATGACGAAATGGTTCGACACTAACTAgtaagtatctggcttgttcatgtgatttgtggtgg--aattgctaacgttgtggaaattttgggcag-------------------------------

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 1
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacattttagctaactggtgctgtttacctttacag
|||| ||||||||  | |  |||  |||||| ||||| ||||| || || |||||||     || |||||||||||||| || ||||| ||||| ||||||||||||  | |||      |  ||| | ||   |  ||    | |  |  |    || ||   ||                                
GGACTGGTGGAGATGTGGCCTTCGACACCTATTTCTCCATGGCGAGAGGGAATGCCAAGCAACCGGCTATGGAGATGACGAAATGGTTCGACACTAACTAgtaagtatctggctagttcatgtgatttgtggtgg--aattgctaacgttgtggaaattttgggcag-------------------------------

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|157650002|gb|EX449636.1|EX449636
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|29636000|gb|CB641009.1|CB641009
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58611543|gb|CK039255.1|CK039255
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|27334367|gb|CA882818.1|CA882818
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58605690|gb|CK033723.1|CK033723
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|29633667|gb|CB638676.1|CB638676
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58664144|gb|CK052830.1|CK052830
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|88360108|gb|CI610222.1|CI610222
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCCAAGTTCTCCTACTCTT
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACC-AAGTTCTCCTACTCTT
EST: gi|117239956|gb|CT849487.1|CT849487
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58686304|gb|CK074991.1|CK074991
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58612621|gb|CK040333.1|CK040333
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58669089|gb|CK057775.1|CK057775
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAAGACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|88358234|gb|CI605159.1|CI605159
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58604596|gb|CK015124.1|CK015124
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACAACAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|300216097|gb|HO088723.1|HO088723
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
EST: gi|58607018|gb|CK035051.1|CK035051
EST:     AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTA                         CCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC
genomic: AATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactt ... acctttacagCCACTTTATCGTCCCTGAACTTGGTCCCAACACCAAGTTCTCCTACTCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCGGTGGAGAGATTGGGTTCAGCACCTACTTCTCGATGGCTAGGGGAAATGCCACTGTCCCTGCTATGGAGATGACCAAGTGGTTTGACACCAACTAgtaagtactttgcttccatttaagatgtctgacagtaaacattttatttaatttttatattcaacattttagctaactggtgctgtttacctttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG