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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaaattggatcttgcgcttcctgccaatttatatgctctacttggaagaagttaaaatggaatttatgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTGAGAGCTGAATAAACTGTGAAGGACATATAAGGCCACTTAGAATGTTCAC

Basic information

species Oryza sativa
transcript LOC_Os01g25370.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G088653_T04 (Zea mays), 3'ss of exon 1
gtaccaaattggatcttgcgcttcctgccaatttatatgctctacttggaagaagttaaaatggaatttatgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTGAGAGCTGAATAAACTGTGAAGGACATATAAGGCCACTTAGAATGTTCAC
                                | ||| | | |   |          | ||||||   |||||| | | |   ||    | || |         ||||||  ||  |||  ||||| || ||||||||||| || | |||||| || ||||||||  ||| ||||||||||||||||||  || |||||||   | | || || |  | |   |
-------------------------------gtaatacgttgtctatcatttttcccataatgga---tatgatgtatctgcaaa----agttgaaa-----caaaattgtatgcattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC
















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|29623085|gb|CB628096.1|CB628096
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|33692526|gb|CF320765.1|CF320765
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|11172767|gb|AU164448.1|AU164448
EST:     GAGATATGGCCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: GAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|218485916|gb|FG967011.1|FG967011
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|29662159|gb|CB658434.1|CB658434
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|29662158|gb|CB658433.1|CB658433
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTGACTTTTGGACAG                         AAACATATGCAT
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCAT
EST: gi|33692527|gb|CF320766.1|CF320766
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|4714382|gb|AU058349.1|AU058349
EST:     GAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: GAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|218499890|gb|FG958714.1|FG958714
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTG
EST: gi|58590052|gb|CF988360.1|CF988360
EST:     TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG                         AAACATATGCATTACTTTCGGAAGA
genomic: TCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaatt ... tctttcatagAAACATATGCATTACTTTCGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTGAGAGCTGAATAAACTGTGAAGGACATATAAGGCCACTTAGAATGTTCAC
                    aattaac  putative branch site (score: 2)
                                          ttgtctttc  putative PPT
     ttttttttcaagtgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaaattggatcttgcgcttcctgccaatttatatgctctacttggaagaagttaaaatggaatttatgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTGAGAGCTGAATAAACTGTGAAGGACATATAAGGCCACTTAGAATGTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA