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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata...

Basic information

species Physcomitrella patens
transcript PP1S79_253V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g28750.1 (Oryza sativa), 5'ss of exon 1
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata-
||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     | | ||| |  ||||||||  |  | |   ||       ||  |  |  | |    |      |     |  |   | |  |  ||  | |   | ||  |  |||    |||| |  
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGCCAGACCTCCACCAAGGGGgtgcgtctctttgctccttccctctctctcactctcagatccagattccctgcaatcc-tgtagccttgccttggtttcttgcaaaaatgatgttttcttc

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 5'ss of exon 2
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtga-attttactgtgtatcgtactttttaatgaattgg-attttata-
||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     | | ||| |  ||||||||||||   |||||   ||       |  | |      || | | | |    || ||| |    |  ||       | | | || |  |||    | | ||  
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGACCTCCACCAAGGGGgtaagccaatccac---gccctcttctagcttccgcgcgtgtgcgccatctgctttgatagcccagagtcgccaaaagtctctagtagattcatgtatcatgt

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 5'ss of exon 2
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata----
||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     | | ||| |  |||||||||||    |  |||||   |  |  | ||||  | | |||   |  |     ||   ||    | | ||     | |  || || |   | ||  | ||    
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAGACCTCCACCAAGGGGgtaagatgatttacttgatgtccctcttccgtcgtcccgttcggttga--ttgtgcagatgcgtcagagtggt-cattggttgat-accggaatcatgtagctg

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA07G37060.1 (Glycine max), 5'ss of exon 2
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatc-gtactttttaatgaattggattttata---------------------------
||| ||||| ||||||||||| || ||||||||||||||||||  |||||||||||| ||||| |||   |||| |||     |||  || |  || ||||||  |   ||  |||  ||| ||  |  || | | |  || | | |   | |  ||||||  | |   || | ||  |||| |||| | |   | || ||                           
GGCTAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCACAAGAATGGCATCAAAAAGCCAAAGAGGCACCGCCACACTTCCACCAAAGGGgtattctcctcttcttttctt-tctctatcgatctacgtttatatattttc-cgatgaattgcatttcatacccgtttttttaaatgtaatttttgttttaatgatttgttgttggcaattcatatag

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G03550.2 (Glycine max), 5'ss of exon 2
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaag-cactgtgaattttactgtgtatcgtactttttaatgaattggattttata-
||| ||||| ||||||||||| || ||||||||||||||||||  ||| |||||||| ||||| |||   |||| ||||    |||  || |  || ||||||     ||| |||   ||  |  ||     |||| | ||| |  | |  || | |  || |  ||  || |  |  |||||  ||       |||| || 
GGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgta-----ttctactcttctctt--atttttatttttattttccgatgattcatttttcatatccct-cgtttatttttttttgttgg--caatttttgtag

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 5'ss of exon 2
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccact----tggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata------------------------
||||||||| |||||||||||||| |||||||||||||||||   |||||||||||| ||||||||       |||||     ||| ||| |  || |||||  |  ||  | ||    |    | |      ||||| |   ||| || | |    |||||  |     |||  |  |    ||| |    |  | | ||  |                        
GGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACCAAAGGGgtttgatttctctctgttttaatctcttccaatcgtttgtttttttccttttacttttgtgatctccttggtgggttttctggtttgagtgctatggtgtttgatttcttttatttgcattggcgtag

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv05s0077g01220.t01 (Vitis vinifera), 5'ss of exon 1
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata-
||||||||| ||||||||||| || |||||||| || ||||||  ||||||||| || |||||||||      || ||     ||   || |  || |||||||   | || |||| | ||    |  |  ||   |  |||| ||| |  | | ||   || |     |    |  | |||    |  || | |  | | 
GGCGAAGTCGAAGAACCACACAGCTCACAACCAATCGTACAAGGCCCACAAGAACGGCATCAAGAAGCCCCGCAAACACCGCCACGCTTCCACCAAAGGGgtaatt-tctcaactttgattt---actcttttccccccttttttctgaagaatatgtgattgatgcgatgaatttgtgttttgaaatctgaaatgaacag

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|19788741|gb|BQ040890.1|BQ040890
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67697573|gb|BJ957806.1|BJ957806
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67693178|gb|BJ953411.1|BJ953411
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7584238|gb|AW700135.1|AW700135
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCANAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67696537|gb|BJ956770.1|BJ956770
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|15729775|gb|BI741482.1|BI741482
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7147953|gb|AW509875.1|AW509875
EST:     GTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: GTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|162268442|gb|FC444315.1|FC444315
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67573153|gb|BJ945977.1|BJ945977
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67569906|gb|BJ942730.1|BJ942730
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7067530|gb|AW497385.1|AW497385
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCATAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67574175|gb|BJ946999.1|BJ946999
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67698803|gb|BJ959036.1|BJ959036
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67508207|gb|BJ941078.1|BJ941078
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67691427|gb|BJ951660.1|BJ951660
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|6166984|gb|AW145255.1|AW145255
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67575340|gb|BJ948164.1|BJ948164
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 175

GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgtttccacttggcttgtcgatgccgtttttcagttttctctaagcactgtgaattttactgtgtatcgtactttttaatgaattggattttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA