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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaacttctacttttgttttatcaacttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG

Basic information

species Oryza sativa
transcript LOC_Os04g56480.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
-taaacttct-acttttgttttatcaacttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG
   |  |||| |  || ||||| ||     |||   |  ||   |||||||  |   |  ||||   | || | ||| |||||    | |||||| |  |||| ||  |||||||||||||||||||||||||||||||||||||||||||||| ||  | ||||||||||| | |||
tccattttctgagattagttttttctg--aatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG

upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 7
taaacttctacttttgttttatcaacttatcatattt-tctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG
  ||  | |   | |||  |||   | | |  | ||  |||  | |||| ||| | |      | |   |||| || | | ||||  |           ||| ||  |||| |||||||||||||| ||  |||| |||||||||||||| |||||  | |||||  | || |||||
ctaatgtttcagtatgtcatattgtcatgtgcttttgatctcatgttat-cttccattttttcttccgggttcaaatttattgcacttgtcttatgcacagATCCCGCTGCTAGTGCTGATCTAGCTGTAGTTCTAATGCAAGAAGGACTGGCACAAATCTTCCTTGTGGGCAGAAG

upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
taaacttctacttttgttttatcaac-ttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctcta----ttagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG
     |    ||| | ||  |   ||   ||  |||||| | |||  |    |    |   ||    | ||||| ||  | ||| |     ||||||    | ||| ||  |||||||||||||| |||||||  || | |||||||||||| | |||||| |  ||||||||||||||||
-----tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG

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|29659831|gb|CB656106.1|CB656106
EST:     GAACTTTGGGATTGGTTAGCTCTTGATACCATCCAACAAGCATGTG                         ACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAACTTTGGGATTGGTTAGCTCTTGATACCATCCAACAAGCATGTGgtatgtgaga ... cctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|58595078|gb|CF993386.1|CF993386
EST:     GAACTTTGGGATTGGTTAGCTCTTGATACCATCCAACAAGCATGTG                         ACCCAACTGCAAGTGC
genomic: GAACTTTGGGATTGGTTAGCTCTTGATACCATCCAACAAGCATGTGgtatgtgaga ... cctctattagACCCAACTGCAAGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG
                                             cctctatt  CT-rich tract
                                      atctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacttctacttttgttttatcaacttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - cttttgt
- - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcatc