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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGGTGACCATGTCTGGCCAGTACTCCGTGAAGAGTGACGTGTACAGCTTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacacagacactgcaccatcaccatttctcctcaatttttctcaagttctcaaaccttgcactgttgcacaatcctctgaactgaactgaactgaactgtattgccccttgctgtctgaacatttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g42626.3
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42626.3 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G121573_T01 (Zea mays), 5'ss of exon 14
CTGAGGTGACCATGTCTGGCCAGTACTCCGTGAAGAGTGACGTGTACAGCTTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacacag---------acactgcaccatcaccatttctc-ctcaatttttctcaagttctc---aaac------cttgcactgttgcac------aatcctctgaactgaactgaactgaactgta----------------ttgccccttgctgtctgaacatttgcag
||||||||| | || |||| ||||||||| ||||||| ||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||||||||||||||| |           ||   |||||||    | |||| | || || |||| || | | |   | ||       |||  |||  | ||      ||   |||||    |  | ||   |  ||||                |   | |||||| ||||||| || ||||
CTGAGGTGATCTTGGCTGGTCAGTACTCCCTGAAGAGCGACGTGTACAGCTTCGGAGTCGTCATGCTAGAGCTTCTGACTGGCCGGAAACCGTTTGACAGgtgaacacagattaatccgctgcagcacaccatctatttctctcacacatttgttctgaactgcgctagagacatgggatttgttctgaagtaccacaagaacaatctgagacaacttaaatgtagttgtagcaacacatacactagtcagcacttgctctctgaactttcgcag

upper sequence: LOC_Os07g42626.3 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S242_37V6.1 (Physcomitrella patens), 5'ss of exon 12
CTGAGGTGACCATGTCTGGCCAGTACTCCGTGAAGAGTGACGTGTACAGCTTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaac----acacagacactgcaccatcaccatttctcctcaatttttctcaagttctcaaaccttgcactgttgcacaatcctctgaactgaactgaactgaactgtattgccccttgctgtct-gaacatttgcag
| ||     ||||||| ||    ||| | |||||||| ||||| ||||||||||| ||||| ||||| ||||| |||||||| ||  | ||||| |||||||  ||    |     ||    ||| |  | |    ||  |   |||   |||  |  |  ||     |  |||   ||   | | || | |  ||||| ||      |  | |  | |||  ||| ||    ||||||
CAGAATACTCCATGTCAGGAACTTACACAGTGAAGAGCGACGTTTACAGCTTCGGCGTTGTGATGCTGGAGCTTCTGACTGGGCGCCAGCCTTTGGACAGgttcactttaatgttaacctctcactag-atcgaaccttttatgtttcattcacttggtttaaggaatccatgtactacttccatatgtatttcactgatcttctgaatcattcttcgtgcaatctcgattgcttgcag

upper sequence: LOC_Os07g42626.3 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S284_52V6.1 (Physcomitrella patens), 5'ss of exon 15
CTGAGGTGACCATGTCTGGCCAGTACTCCGTGAAGAGTGACGTGTACAGCTTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacacagacactgcaccatcaccatttctcctcaatttttctcaagttctcaaaccttgcactgttgcacaatcctctgaactgaactgaactgaactgtattgccccttgctgtctgaacatttgcag
||||     |||||| |||    ||| | |||||||||||  | || |||||||| ||||| ||||||||||| || ||||| || || |||||||||||||       | ||   ||  |        || ||  ||||||   | |   |      |   |   | ||||     | || | ||   ||| |||    |    |   | |  || |                
CTGAATACGCCATGTTTGGAACTTACACTGTGAAGAGTGATATTTATAGCTTCGGCGTTGTGATGCTAGAGCTTCTCACTGGGCGAAAGCCTTTTGACAGgtt------ctgattttgttc--------ttccttgtcaattaaccccttataacttcattcttttcagttg----gttctttcaataaaaccgaaactcatgaaaagtcgctctgtt----------------

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|87021411|gb|CI274018.1|CI274018
EST:     TTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAG                         ATCCCGGCCACGGTCGGAGCAGTCACTGGTCGGGTGGGCAACTCCCCAGCT
genomic: TTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacac ... acatttgcagATCCCGGCCACGGTCGGAGCAGTCACTGGTCGGGTGGGCAACTCCCCAGCT
EST: gi|87007926|gb|CI296904.1|CI296904
EST:     TTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAG                         ATCCCGGCCACGGTCGGAGCAGTCACTGGTCGGGTGGGCAACTCCCCAGCT
genomic: TTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacac ... acatttgcagATCCCGGCCACGGTCGGAGCAGTCACTGGTCGGGTGGGCAACTCCCCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGGTGACCATGTCTGGCCAGTACTCCGTGAAGAGTGACGTGTACAGCTTCGGTGTTGTCATGCTAGAGCTCCTGACTGGCCGGAAACCTTTTGACAGgtgaacacacagacactgcaccatcaccatttctcctcaatttttctcaagttctcaaaccttgcactgttgcacaatcctctgaactgaactgaactgaactgtattgccccttgctgtctgaacatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT