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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatttttctatttcccttcaaagtttctgctactgctgctttataactttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 13
gttcatttttctatttcccttcaaagtttctgctactgctgctttataac--tttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG
  ||||| |||||| | ||| | |  || ||| || |     ||| |||   |||  |||||||| || |  ||   |||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||| 
-gtcattcttctatctgcctccgagtttgctgttattaacagtttttaaagattttggttgcactcacttaaattccatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAT

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G305559_T01 (Zea mays), 3'ss of exon 3
gttcatttttctatttcccttcaaagtttctgctactgctgctttataac--tttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG
  ||||| |||||| | |||      || ||| || |     ||| |||   |||  |||||||| || |  ||  ||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||||
-gtcattcttctatctgcctctggttttgctgttattaacagtttttaaagattttggttgcactcacttaaattcaatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G481395_T01 (Zea mays), 3'ss of exon 3
gttcatttttctatttcccttcaaagtttctgctactgctgctttataac--tttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG----
  ||||| |||||| | |||      || ||| || |     ||| |||   |||  |||||||| || |  ||  ||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||| ||    
-gtcattcttctatctgcctctggttttgctgttattaacagtttttaaagattttggttgcactcacttaaattcaatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGC-CCTCAGCTCCGAGCGGCCCTTGTTAAACTATAGGTAA

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G422539_T01 (Zea mays), 3'ss of exon 3
gttcatttttctatttcccttcaaagtttctgctactgctgctttataac--tttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG
  ||||| |||||| | |||      || ||| || |     ||| |||   |||  |||||||| || |  ||  ||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||||
-gtcattcttctatctgcctctggttttgctgttattaacagtttttaaagattttcgttgcactcacttaaattcaatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 12
gttcatttttctatttcccttcaaagtttctgctactg-ctgctttataactttcagttgcacttacct----tgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG
  ||||| |||||| |  || |||  || |||||| || | | |||| |  ||||  ||||||| || |    ||||  ||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||
-gtcattcttctatctggctccaagtttcctgctattgacagttttaaagatttcgtttgcactcacttcaattgattcaatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG

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|88215064|gb|CI214913.1|CI214913
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88489314|gb|CI426586.1|CI426586
EST:     CTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: CTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88831123|gb|CI080547.1|CI080547
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTGGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88536315|gb|CI466060.1|CI466060
EST:     TCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: TCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88526548|gb|CI454616.1|CI454616
EST:     CTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: CTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88994093|gb|CI116057.1|CI116057
EST:     CGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCCAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: CGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88248064|gb|CI246682.1|CI246682
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|86903727|gb|CI300581.1|CI300581
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|86259979|gb|CI065852.1|CI065852
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|86865883|gb|CI335514.1|CI335514
EST:     CTTCTGAGTTTTTGTCTGAACCTTGTCACTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: CTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|86490395|gb|CI133028.1|CI133028
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88223219|gb|CI223068.1|CI223068
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88845492|gb|CI084417.1|CI084417
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTGGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|29634138|gb|CB639147.1|CB639147
EST:     GTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: GTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88480857|gb|CI418128.1|CI418128
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|88837192|gb|CI078552.1|CI078552
EST:     ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: ACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|89177897|gb|CI391076.1|CI391076
EST:     GAGTTTTTGTCTGAACCTTGTCACGTCGGGCATTTGAATTTCAG                         GCTGATCCTTTTGCCAAGAACCTTGGGTATCCTCCTCAGCTCCGTGCAGCC
genomic: GAGTTTTTGTCTGAACCTTGTCA-GTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
EST: gi|89171171|gb|CI109695.1|CI109695
EST:     CGTTCTGAGTTTTTGTCGTGAACCTTGTCAGTCGGGCATTTGAATTTCAG                         GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC
genomic: CCTTCTGAGTTTTTGTC-TGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 66 (downstream exon)
Score: 40

CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcattttt ... taatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctactgctgctttataactttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG
                                                tttct  CT-rich tract
                                       ttgatataatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatttttctatttcccttcaaagtttctgctactgctgctttataactttcagttgcacttaccttgatataatttctagGCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC