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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgccacttttcccttattcttcatgtcggatgattcatatgattttgcatgatgtgagctggtgcctggtggcaatactgcag

Basic information

species Oryza sativa
transcript LOC_Os04g35520.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35520.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G120517_T03 (Zea mays), 5'ss of exon 8
---AATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgccacttttcccttattc---ttcatgtcggatg--attcatatgattttgcat-gatgtgagctggtgcctggtggc-aatactgcag-----
   ||||| ||||||||||||||||||||||| ||||||| ||||||||| | ||||||||||||||| ||||||||  |||||   ||     |   |      ||||  |  |  ||       |   |||   | || |  |    |||   | || ||||    ||     
AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgccttgttatgtatggccaagcctatgttaggcgcaatagggccaaggctgcccaggtggggcccaaggcccaatagctaatagataagctcta

upper sequence: LOC_Os04g35520.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G120517_T01 (Zea mays), 5'ss of exon 8
----------------------------AATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgccacttttcccttattc---ttcatgtcggatg--attcatatgattttgcat-gatgtgagctggtgcctggtggc-aatactgcag-----
                            ||||| ||||||||||||||||||||||| ||||||| ||||||||| | ||||||||||||||| ||||||||  |||||   ||     |   |      ||||  |  |  ||       |   |||   | || |  |    |||   | || ||||    ||     
TACTATGTCTTGTTACTCTTTACAGAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgccttgttatgtatggccaagcctatgttaggcgcaatagggccaaggctgcccaggtggggcccaaggcccaatagctaatagataagctcta
















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|29662488|gb|CB658763.1|CB658763
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|27553941|gb|CA997841.1|CA997841
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|88228841|gb|CI226692.1|CI226692
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|88326055|gb|CI651106.1|CI651106
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTCATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGCTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|116875540|gb|EC366048.1|EC366048
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACGGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|29655600|gb|CB651875.1|CB651875
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|29670965|gb|CB667240.1|CB667240
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|33683886|gb|CF312125.1|CF312125
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGTGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|58611888|gb|CK039600.1|CK039600
EST:     TCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACGGATGCT
genomic: TCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|89177225|gb|CI043728.1|CI043728
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|116875560|gb|EC366068.1|EC366068
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACGGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|58672863|gb|CK061549.1|CK061549
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTA
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTA
EST: gi|86522629|gb|CI162835.1|CI162835
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
EST: gi|86496471|gb|CI139104.1|CI139104
EST:     GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG                         GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT
genomic: GGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgcca ... aatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAGgtacgtgccacttttcccttattcttcatgtcggatgattcatatgattttgcatgatgtgagctggtgcctggtggcaatactgcag

- - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - -  AGCTGA