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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttctcaatcttgatgggagtttttccctagaatgttgctttgatcccctgcctaaacacagaacaaattcaccttttattttcttttactacaagtgctgaatcatccttccaaacttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACACTCACCGCAGATGAGATAAACAAAGTGGTTCATCCCTACCAAGAAGAGC

Basic information

species Oryza sativa
transcript LOC_Os01g43150.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 16
gtatgtttctcaatcttgatgggagtttttccctagaatgttgctttgatcccctgcctaaacacagaacaaattcaccttttattttcttttactacaagtgctgaatcatccttccaaacttc-ttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACACTCACCGCAGATGAGATAAACAAAGTGGTTCATCCCTACCAAGAAGAGC
|| ||| || |||   |||| |  ||| |  | |||| ||        ||| | | |    |||    ||    ||   |||      |||        | |||||| |||   ||||||||||  || ||||||||||||||||||||| ||| ||||||| || ||||||||||||||||| || || ||||||||||| |||||||| ||||| || |||||||||||||
gtttgtctcacaactgtgattg--gttctgtcgtagagtg--------atcactttc----acatgataccggatcctttttagcgcactt--------aatgctgagtcaattttccaaactttgttttcagCATGAGAAGCAATTACATGCTCTAGCAAATGCGCTGCTGGAGCGTGAAACGCTTACTGCAGATGAGATCAACAAAGTAGTTCACCCTTACCAAGAAGAGC

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 16
gtatgtttctcaatcttgatgggagtttttccctagaatgttgctttgatcccctgcctaaacacagaacaaattcaccttttattttcttttactacaagtgctgaatcatccttccaaacttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACACTCACCGCAGATGAGATAAACAAAGTGGTTCATCCCTACCAAGAAGAGC
                          || | | ||  |   |||   |   |  || || | | | |  ||  |  |  |||| ||||  | ||||   | ||| ||  |||  | | ||  || || ||||||||||||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||||||||| |||||||| ||||| || ||||||||||| |
--------------------------ttcttcttaatacaatgcccgggggc--tgtcttacccccg--caggtcaagttttttttttagtgtactt--aatgccgatacattttccaaactttgttttcagCATGAGAAGCAATTACATGCTTTGGCAAATGCGCTGCTGGAGCGTGAAACACTTACTGCAGATGAGATCAACAAAGTAGTTCACCCTTACCAAGAAGAAC
















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|29623582|gb|CB628593.1|CB628593
EST:     TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|29672103|gb|CB668378.1|CB668378
EST:     TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|88217561|gb|CI217410.1|CI217410
EST:     TTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|25806971|gb|CA762932.1|CA762932
EST:     TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|33684137|gb|CF312376.1|CF312376
EST:     TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|29623624|gb|CB628635.1|CB628635
EST:     TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TCAAACTCTTAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
EST: gi|89198534|gb|CI016619.1|CI016619
EST:     TAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAG                         CATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA
genomic: TAAGAGAAGCTTATGGGCGGGTCAAGCGTTTATTGAAGAAGgtatgtttct ... ttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttattttcttttactacaagtgctgaatcatccttccaaacttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACACTCACCGCAGATGAGATAAACAAAGTGGTTCATCCCTACCAAGAAGAGC
                                            cttcttgtc  CT-rich tract
     tattttcttttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttctcaatcttgatgggagtttttccctagaatgttgctttgatcccctgcctaaacacagaacaaattcaccttttattttcttttactacaagtgctgaatcatccttccaaacttcttgtcagCATGAGAAGCAATTACACGCTTTAGCAAACGCCCTGCTGGAGCGTGAAACACTCACCGCAGATGAGATAAACAAAGTGGTTCATCCCTACCAAGAAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG