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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaggggggaagaggggtctctcggtttgagctctcacgcggatgctttttctttttcttttttgaaaggaaaaattgggtgggttttgaaggggtactgattgatcggttgggttgctgatgagtggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG

Basic information

species Oryza sativa
transcript LOC_Os11g14010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 1
gtatggaggggggaagaggggtctctcggtttgagctctcacgcggatgctttttctttttcttttttgaaaggaaaaattgggtgggttttgaaggggtactgattgatcggttgggttgctgatgagtggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
                            ||  | ||   | |        |||  |    ||  |   | ||    |   |  ||| |    |  | ||      | | ||| |||| || |||               | |||| ||  ||||||| || | ||  ||  |        |||||| ||||||||||||||||||||||| |||||||
----------------------------gtacgcgcctgctccttacccatttccccccctccctcgcggaatttgaggatttgtgaggcccgcggaggct----tcgctcgattggtttcctg---------------gcggctaat--tggtttgatttggttgcttcct--------tgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG

upper sequence: LOC_Os11g14010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008259_T01 (Zea mays), 3'ss of exon 1
gtatggaggggggaagaggggtctctcggtttgagctctcacgcggatgctttttctttttcttttttgaaaggaaaaattgggtgggttttgaaggggtactgattgatcggttgggttgctgatgagtggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG-------------------------------------------------------------------
                            ||  | ||   | |        |||  |    ||  |   | ||    |   |  ||| |    |  | ||      | | ||| |||| || |||               | |||| ||  ||||||| || | ||  ||  |        |||||| ||||||||||||||||||||||| |||||||                                                                   
----------------------------gtacgcgcctgctccttacccatttccccccctccctcgcggaatttgaggatttgtgaggcccgcggaggct----tcgctcgattggtttcctg---------------gcggctaat--tggtttgatttggttgcttcct--------tgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGGTGAGCTCGCGCGCGCGCGCGTTCCTCCGATTCGCCGCGCCCGTGCCTCGGATTCGCACGATTCGGT
















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|32948276|gb|BP184848.1|BP184848
EST:     CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAG                         ATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
genomic: CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAGgtatggaggg ... tcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
EST: gi|58678314|gb|CK067001.1|CK067001
EST:     CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAG                         ATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
genomic: CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAGgtatggaggg ... tcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
EST: gi|58675845|gb|CK064532.1|CK064532
EST:     CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAG                         ATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
genomic: CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAGgtatggaggg ... tcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
EST: gi|426996|gb|D23072.1|D23072
EST:     CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAG                         ATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
genomic: CCGGGACTTCCGCGCGCGGCGGGCCGGGATGATCAAGGCGCTGACCACAGgtatggaggg ... tcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
           ggctgat  putative branch site (score: 4)
                                 tttttttttgtttctt  putative PPT
                                atttttttttgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaggggggaagaggggtctctcggtttgagctctcacgcggatgctttttctttttcttttttgaaaggaaaaattgggtgggttttgaaggggtactgattgatcggttgggttgctgatgagtggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT