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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA

Basic information

species Oryza sativa
transcript LOC_Os06g03760.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 3
--gtgcctatattctcacatacttcttttcaattatga-----------------gcattcattagaaccatatttttctactac-ata-taattatcactt-tgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
  | || || |||||||  |||  | |||  || || |                 |  |   ||   | || || ||| |  | | ||| |||||||   || |     | |||||||   |||||  | ||||| | | |||||||||||||||||||| || ||||||||  |||| || || ||||| ||||||||||| ||||||||||| | ||||||||| |||||| | ||||||||||
gtgggcatacattctcatgtacaacattttgatcataacggaaaaacggatgcttgtgtctcttgtgatca-atctttttgttgctatagtaattattgattgttcggatatcaatgtttcttgaggttaaacatgtatcctgcagGAAGCAACTGAACTGGGAAAGAAGGCCAGGGAGTTAAAAAAAGCTGCTGAAGCCCTACACCAAGAAGAAAGAAGTGGGAACAAGGGCCGGAAATGGCGCA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 5
--gtgcctatattctcacatacttcttttcaattatgagca--------ttcattagaaccatatttttctactac-ata-taattatcactt-tgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
  | || || |||||||  |||  | |||  || || |            ||||| |      || |||||| | | ||| ||||| |   || |     | |||||||    |     | || || |   |||||||||||||||||| | || ||||||||  ||||  |||| || || |||||||| |||||||||||||| | ||||||||| |||||| | |||||||| |
gtgggcatacattctcatgtacaccattttgatcataaaggatgcttgcctcatttgtgatcaatctttctattgctatagtaattgttgattgtttggatatcaatgtttccttgaggttaaaatctgccctgcagGAAGCAACTGAATTGGGGAAGAAGGCCAGGGAGCTGAAAAAGGCGGCTGAAGCTCTTCACCAAGAAGAAAGAAGTGGGAACAAGGGCCGGAAATGGCGAA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
                               |||  || || || || |  | |  |    | ||   ||        || |   || || | ||||   |  | |||   ||  |   ||||||||||||||||||| ||||| || ||    ||| ||||||||||||||||| | ||||| || ||||| | ||||||   |||||| || ||||  || |
---------------------------gtgctatatgcttttat-agcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggtt-ggctggttatggt---tgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttga--aattttcaatgtggattga--gactgaacat---att-ttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
         |||     | ||  || |   || |   | |   ||    | |   |||||||    ||| |  || ||||| |   | ||  || |||   | |   |||    |||   ||| || | ||||||||||||||||||||||| |||||  | ||  | |||||||||||||| || |||||||| |||||   ||||||    ||||| || || ||| | |
--------gttcatttgtgctggttattg-ttgtctacttgtcttcatgcaaagcttttctaaagaatacatgta-cacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA

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|58680419|gb|CK069106.1|CK069106
EST:     CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATCACG                         GAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAA
genomic: CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAGgtgcctatat ... ttttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAA
EST: gi|88730217|gb|CI753832.1|CI753832
EST:     CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG                         GAAGCAACTGAACTAGGTAAGAAGGCT
genomic: CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAGgtgcctatat ... ttttctgcagGAAGCAACTGAACTAGGTAAGAAGGCT
EST: gi|33381043|gb|CF196386.1|CF196386
EST:     CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG                         GAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAA
genomic: CATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAGgtgcctatat ... ttttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
                                           tattttct  CT-rich tract
          tttgaaattttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG