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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccaccccccctcctcttcttttcccctccacaacctctccatcccttgccttcatgaatcagtattgtagattccccatctagctgtttaacccg...

Basic information

species Oryza sativa
transcript LOC_Os01g73880.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G113096_T01 (Zea mays), 5'ss of exon 1
CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtt--tcccaccccccctcctcttcttttcccctccacaacctctccatcccttgccttcatgaa-tcagtattgtagattccccatctagctgtttaacccg
|||||||||||||||||||||| || |||  ||||  |||  ||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||| |||   ||| ||   | |||     |   | | | || |     |||| | || | |  |||     |||  | |   | | |    || || |    ||    
CCTTCTGGTTCGACAACCCGCACGGCAAGAACAAGATGGCCGCCTGGGGGAGCTCCATCCGACCCATCCACACCTTCTCCACCGTAGAGGACTTCTGGGGgtgcgtccgactatctctctctgacacatgcacacctcttaacctcctttccctcctctcacactctcacaactactggtacaa-gtccagattcacaata--

upper sequence: LOC_Os01g73880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G002616_T01 (Zea mays), 5'ss of exon 1
CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccaccccccctcctcttcttttcccctccacaacctctccatcccttgccttcatgaatcagtattgtagattccccatctagctgtttaacccg
||||||||||||||||||||||| | ||||||||||||||  ||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||| |||         | | ||   |||     |||||  |   || |||    |      ||      || | ||     || ||  |  |  |  |    |||
CCTTCTGGTTCGACAACCCGCAGAGCAAGTCCAAGCAGGCCGCCTGGGGGAGCTCCATCCGCCCCATACACACCTTCTCCACCGTCGAGGAATTCTGGGGgtgcgttcattctcttcagattcgccctccctcgtccttctatcctcttcccctgatcgcatcccactgtttctcttttccgttacaaatcctccgaccg

upper sequence: LOC_Os01g73880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 1
CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtt----tcccaccc---cccctcctcttct-----tttcccctccacaacctctccatcccttgccttcatgaatcagtattgtagattccccatctagctgtttaacccg-------------
|||||||||||||||||||    |  |||||||| || ||  | ||||| ||||||||||| |||||| |||| ||| |||||||||| || || |||||||     | | | |    ||| |||| |||      ||| |||||  |    |||  | |   |  |||| |   | | ||||| |  |||     || | | |||                   
CCTTCTGGTTCGACAACCCTTCCGCCAAGTCCAAACAAGCTGCATGGGGCAGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttcgatcttttcccttccttttcccccaattttccctcttctgggtcttaacctaattgcttctttcttgattattggaagttctgacccttgtttttttgttttaaaatttgttcag

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|88395227|gb|CI609543.1|CI609543
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|86854076|gb|CI252067.1|CI252067
EST:     CTCCATCCGCCCCCATCCAAAACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: CTCCATCCG-CCCCATCC-ACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|88593112|gb|CI711266.1|CI711266
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCA
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCA
EST: gi|427733|gb|D23868.1|D23868
EST:     AGCTCCATCCGCCCCATCCACACCTTCTACACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|14571254|gb|BI118622.1|BI118622
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|88692539|gb|CI736114.1|CI736114
EST:     GCTCCANTCCGCCC-ATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATC
genomic: GCTCCA-TCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATC
EST: gi|14571263|gb|BI118631.1|BI118631
EST:     GGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|88427183|gb|CI586731.1|CI586731
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|66922020|gb|CX108868.1|CX108868
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|27578259|gb|CB000954.1|CB000954
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|88765509|gb|CI774603.1|CI774603
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|8858103|gb|AU095421.1|AU095421
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGAAG                         CCTTTATACCAATATCCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATAT-CCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACT
EST: gi|88406261|gb|CI596388.1|CI596388
EST:     AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTT
EST: gi|88727789|gb|CI749591.1|CI749591
EST:     AGCTCCATCCGCCCCATCCANACCTTCTCCACCGTCGAGGACTTCTGGAG                         CCTTTATAACAATATCC
genomic: AGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCC

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: 69 (upstream exon), 74 (downstream exon)
Score: 33

CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccacc ... ggtatttcagCCTTTATAACAATATCCATCACCCAAGCAAGTTGGTTGTGGGAGCTGACTTCCATTGCTTTAAGAATAAAATCGAGCCAAAATGGGAAGATCCTATCTGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtttcccaccccccctcctcttcttttcccctccacaacctctccatcccttgccttcatgaatcagtattgtagattccccatctagctgtttaacccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccatc