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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaggttgaccaccttgaagtactccccagatgtttctgctctgcttttgcttcatatagctgtcgtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g14932.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G180065_T01 (Zea mays), 3'ss of exon 6
gtaagcaggttgaccaccttgaagtactc------------cccagatgtttctgctctg------cttttgcttcatatagctgtcgtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG
|||| | |  || ||   |  |  ||  |            |||||   ||| |  ||||      | ||  | |  ||   ||| | |  || ||||||||| ||||| ||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||
gtaatctgaatgtccttttacatttagccatgggtccatggcccagcaatttattttctgaatttaccttcaccttgtacttctggcctttttgcagGTATGTTGCACCGGAGTACGCCATGACAGGACACTTGCTTGTAAAAAGTGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTAACTGGGAGGAGG

upper sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 5
-gtaagcaggttgaccaccttgaagtactccccagatgtttctgctctgcttttgcttcatatagctgtcgtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG
  ||      ||     | ||    ||||    |  |   | |  | |   |||       |  |     ||   |  ||||||||||| || || ||||| ||||| |||||| |||| || ||||||||||| |||||||| || |||||  | || |||||  | |  || ||||  
gttagtttcattcttttctttcttatacttgttattttcatttaatttaaatttaagatgaaatgaaactgt-tatatagGTATGTAGCGCCTGAATATGCTATGACTGGACACCTGCTAGTTAAAAGCGATGTTTATAGCTACGGCGTTGTCTTGCTGGAACTGTTGATCGGAAGGAAA

upper sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G01520.1 (Glycine max), 3'ss of exon 5
gtaagcaggttgaccaccttgaagtactccccagatgtttctgctctgcttttgcttcatat--agctgtcgtgcttt-cagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG
      || || |     ||          || | | |||    |    |||   || | ||  |       || | |  ||||||||||| || |||||||| ||||| |||||| | ||||| |||||||| || |||||||| || |||||  | || |||||  | || || ||||  
---gttagtttcattctattatttcttatacctgttattttcatttaattttgatttaagatgaaatgaaactgttatgtagGTATGTAGCGCCCGAGTATGCCATGACCGGACACCTACTTGTTAAAAGCGACGTTTATAGCTACGGGGTTGTCTTGCTGGAACTGTTGACCGGAAGGAAA

upper sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0005g01590.t01 (Vitis vinifera), 3'ss of exon 5
-gtaagcaggttgac-caccttgaagtactccccagatgtt-tctgctctgcttttgcttcatatagctgtcgtgcttt-cagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG
  |   ||   |  | || |||       |  |    | ||  ||  | |  | |    | || |  ||    || ||| |||||||||||| || |||||||| ||||| |||||  | || |||||||| ||||| || |||||||||||||| || |||||  |  | || ||||| |||
gtttgtcatactctctcatcttttgtccttaacttagtattacctagtttaatgtgtagtaatgttactaaattggtttacagGTATGTAGCCCCTGAGTATGCTATGACTGGACATCTACTAGTAAAAAGTGATGTTTACAGCTATGGAGTTGTCCTCCTTGAGTTGTTGACAGGGAGAAGG

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|29625207|gb|CB630218.1|CB630218
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|88902229|gb|CI374837.1|CI374837
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACCTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|29619813|gb|CB624825.1|CB624825
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|58681155|gb|CK069842.1|CK069842
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|29628587|gb|CB633598.1|CB633598
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactccccagatgtttctgctctgcttttgcttcatatagctgtcgtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG
                                              tgctttc  CT-rich tract
                               ttcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaggttgaccaccttgaagtactccccagatgtttctgctctgcttttgcttcatatagctgtcgtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG