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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTATTGACTGCAAGTACTTCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagctatatctttacatgctataaacatgtgaattcagtgctactaatgtacttttgtggcttgtcatcaacataaatctcactagctatccaga...

Basic information

species Oryza sativa
transcript LOC_Os06g21390.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G395842_T02 (Zea mays), 5'ss of exon 4
GTCTATTGACTGCAAGTACTTCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagctatatctttacatgctataaacatgtgaattcagtgctact-aatgtacttttgtggcttgtcatcaacataaatctcactagctatccaga---
||||||||| |||||||||||||| ||||| |||||  | || ||||| ||  |||| |||||||| ||||||| ||  |     |||||||||||| |  ||||||| | | |||  || ||  ||||||   | || |  | |||  |   |||   | |||| |  ||   
GTCTATTGATTGCAAGTACTTCGACTTTGGGACTGGCTCATGCCCCTTCGGAACAAGTTGTTTCTATAAGgtaggaatattgtcttttacatgctatga-tatgtgaagtgaatgcagctgaacatactttgaggtctggagaccaagtt---tctttttggctaacatgattt

upper sequence: LOC_Os06g21390.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0064g01090.t01 (Vitis vinifera), 5'ss of exon 5
GTCTATTGACTGCAAGTACTTCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagctatatctttacatgctataaacatgtgaattcagtg--ctactaatgt--acttttgtggcttgtcatcaacataaatctc--actagctatccaga
|||||||||||||||| |||| |||||||||| ||| || || || |||||  | || ||||| ||||||||| ||   | | |  | |       |||  ||||  | |  ||   || || || |  | ||     | || | |  | |||  | ||   ||| |   ||    
GTCTATTGACTGCAAGCACTTTGATTTTGGAAATGGGACATGCCCTTTTGGCACTAGTTGTTTTTACAAGgtaaaa---tttgttgtcatgcttgttaattatgtagagtatgttttcttctcatctggagttcaactgattataaatagcatttagctggaacttgtcttct---
















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|86503227|gb|CI145860.1|CI145860
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAACCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGTTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86505760|gb|CI148393.1|CI148393
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|88230758|gb|CI230634.1|CI230634
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACACCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86492751|gb|CI135384.1|CI135384
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTATTGACTGCAAGTACTTCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagctatatctttacatgctataaacatgtgaattcagtgctactaatgtacttttgtggcttgtcatcaacataaatctcactagctatccaga

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT