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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTATCTGGATTGGAATGCTTCTTAATGGATCCTGACTCGTTAGCTTCTGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacctatccctggtctttatttcttgataataaacaaaacaagggtagaactttgtggatgataaagaacatttacaatctggcatattttttccag

Basic information

species Oryza sativa
transcript LOC_Os02g35160.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35160.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G128189_T01 (Zea mays), 5'ss of exon 9
CGGCTATCTGGATTGGAATGCTTCTTAATGGATCCTGACTCGTTAGCTTCTGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttg--taaccta--tccctggtctttatttcttgataataaacaaaacaagggtagaactttgtggatgataaagaacatttacaatctggcatattttttccag
||||| |||||  | || || ||| | ||||||||||| || || ||||||||||| ||||| || ||||||||||||||||||||||| ||||||||||||    |  ||||  ||||| || | ||| |  ||    | | || |  |    |||     |||| | || | | |  |  | || ||   ||      || |||
CGGCTTTCTGGGCTCGAGTGTTTCCTGATGGATCCTGATTCATTGGCTTCTGAGCTCCAGAAAAAATTTGCTTGCAGCACCACCACAGCAGAGCTTCCAGgtaacttggcctacatcccttgt-tgtatcttctgtccttgagcagactagttatag-----tgtgaaggaaatacattacatccactcca-cacgaccatttcag

upper sequence: LOC_Os02g35160.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA12G37040.1 (Glycine max), 5'ss of exon 8
CGGCTATCTGGATTGGAATGCTTCTTAATGGATCCTGACTCGTTAGCTTCTGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacctatccctggtctttatttcttgataataaacaaaacaagggtagaactttgtggatgataaagaacatttacaatctggcatattttttccag--
   || |||||  ||||||  ||  | || ||| ||||  | || || || || ||||||||||||||||||||||| |||||    || || || ||||||    |  | |   | |  || |  |    |   | |      |  | |      | |    | || | |    | |||| | |      || | ||      
AAACTCTCTGGTATGGAATCTTTTCTTATAGATGCTGAAGCATTGGCATCAGAACTGCAGAAGAAGTTTGCTTGCAGTACCACTGTTGCAGAACTACCAGgt----atttcttggttgcattgaaattacaagttttattttggcgtgcgctttgttatcctcaagaaatatgggacttacgagcatatgaatgtctttgttcc
















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|29624720|gb|CB629731.1|CB629731
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|88831299|gb|CI082109.1|CI082109
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|88842138|gb|CI081394.1|CI081394
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|89171258|gb|CI109782.1|CI109782
EST:     AGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGTTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: AGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|58588169|gb|CF986477.1|CF986477
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGGGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|88295867|gb|CI532828.1|CI532828
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|58669317|gb|CK058003.1|CK058003
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|89173075|gb|CI040968.1|CI040968
EST:     CACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: CACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|88468179|gb|CI517638.1|CI517638
EST:     GTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: GTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|88843052|gb|CI371952.1|CI371952
EST:     CAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: CAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|29628424|gb|CB633435.1|CB633435
EST:     TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: TGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
EST: gi|86842093|gb|CI338447.1|CI338447
EST:     CACAGCTGAGCTTCCAG                         GTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC
genomic: CACAGCTGAGCTTCCAGgttgtaacct ... ttttttccagGTAAGAAAGGGCAACACGAGGTCTTGGTTCAAGGTGGAGTCATCGATGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTATCTGGATTGGAATGCTTCTTAATGGATCCTGACTCGTTAGCTTCTGAGCTGCAGAAGAAGTTTGCTTGCAGCACCACCACAGCTGAGCTTCCAGgttgtaacctatccctggtctttatttcttgataataaacaaaacaagggtagaactttgtggatgataaagaacatttacaatctggcatattttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT