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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag

Basic information

species Physcomitrella patens
transcript PP1S490_20V6.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os12g41220.1 (Oryza sativa), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgta-accaccatgttcatgttgtggctttgatgctcttcttcaccgtctgt-attcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
| |||| || |||||||||||||||||||| || | |||||||||||| | ||| || ||  | |||||||||||   ||| ||| | ||||  |||||||||   ||| |      || |   |  ||  | ||     |     ||  | ||| | |    |    | ||  |||  ||| | | | ||||                                   
ACTGAAGCTTTTCTGCGACAAGGACTACCCAGACAGGCCACCAACTGTAAAATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacgagaaatttggttcagaattatttctaactcttgtgttcaattatttgattaattaa--aacttatcttttgg-agctaatgtag----------------------------------

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os09g12570.1 (Oryza sativa), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
  |||| |||||||| |||||||||||||| || ||||||||| ||||  | || |||||  | ||||| ||| |   ||| ||    ||||| |||  ||||  | |      ||  | || | |   | | |  | |     ||      |    |  ||| |    || ||   |||    | |||     | ||                            
GCTGAAGCTGTTCTGTGACAAGGACTACCCAGAGAAGCCACCATCTGTCCGGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctcctcccaaat-gtagatgccaagtttatttattttgtgcaggctactccctctgattga-tattcatttggtg--ctgtgatcctatag----------------------------

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G056501_T05 (Zea mays), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccac--catgttcatgttgtggct-ttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
  ||||  |||||||||||||||||||||| || ||||||||| | ||| |||| |||||  | || ||| | ||    || ||    || || ||| |||||||| |  |||||   ||| || |   ||| |||        |   || |  || | | |   |   | ||  |||| |         | ||    |    |                         
GCTGAAGTTGTTCTGCGACAAGGACTACCCTGAGAAGCCACCATCAGTTCGATTTCATTCAAGAATAAACTTAACATGCGTTAATCATGAAACTGGAGTGgtaacctcttcatgtctttgtggttgtggttggtgcagaatactagtttcag-gtttgatatttgggataccttctctgattttgctatatctattttggttgag------------------------

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G056501_T02 (Zea mays), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaact--gtcagtatcatgcatttcgtag
  ||||  |||||||||||||||||||||| || ||||||||| | ||| |||| |||||  | || ||| | ||    || ||    || || ||| |||||||| |    |   | |||||| | || |  |  |    |      || |  | | |  | ||  |     || ||     |   | |    | | |||  |  ||     ||||| |        
GCTGAAGTTGTTCTGCGACAAGGACTACCCTGAGAAGCCACCATCAGTTCGATTTCATTCAAGAATAAACTTAACATGCGTTAATCATGAAACTGGAGTGgtaacctcttcatgtct-ttgtggttgtggt--tggtgcagaatactagtttcaggtttgatatttgggataccttct-----ctgattttgctatatctattttggttgaggtcatgtag-------

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ33318 (Selaginella moellendorffii), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtct-gtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
| | ||  ||| ||||||||| ||||| || ||||||||||||| |||  |||||||||| || ||||||||||||   || ||    ||||| |||   |||| |||     ||   ||      ||| | ||   |||    |||| || |  | | |    |||  |||||   ||    ||  ||| |  |||  ||  || |   | |  ||||        
ACTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGACTTGCGTTAATCGCGAGACTGGAGCTgtaagcac-----tcgcatt------ttgtttcttggctttgtggtctagtttctggtgt----ttccactagtgatctt---acttgtgcagtaagcactcgcttttt-ttttttgca--------

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ15952 (Selaginella moellendorffii), 5'ss of exon 3
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccac-catgttc-atgttgtggctttgatg-ctcttcttcaccgtctgtattcgctctcctgttcagctagtctgc---tggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
  | ||  ||| ||||||||| ||||| || ||||||||||||| |||  |||||||||| || ||||||||||||   || ||    ||||| |||   |||| ||| |   ||   | |  ||||||||  | ||  | |     || |  | | |   || |  |     |||  ||    |||  || ||||                                    
GCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGACTTGCGTTAATCGCGAGACTGGAGCTgtaagcactcgcattttgtttcttggctttgtggtctagtttctggtgtttccactagtgatcttacttgtgcagtaagcactcggcctccggtgttttc--------------------------------

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|208363724|gb|DC954695.1|DC954695
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162260754|gb|FC435406.1|FC435406
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|208365088|gb|DC947324.1|DC947324
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67698924|gb|BJ959157.1|BJ959157
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37843398|gb|BJ601406.1|BJ601406
EST:     CGGATCAACATGACTCATGTGAACTCGGAGACGGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
genomic: CGGATCAACATGACTCATGTGAACTCGGAGAC-GGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
EST: gi|162248627|gb|FC424480.1|FC424480
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162211664|gb|FC387952.1|FC387952
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162277404|gb|FC453210.1|FC453210
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37840937|gb|BJ598945.1|BJ598945
EST:     GATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162224431|gb|FC399807.1|FC399807
EST:     ATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: ATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162277403|gb|FC453209.1|FC453209
EST:     AGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: AGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162176507|gb|FC352976.1|FC352976
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162260755|gb|FC435407.1|FC435407
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67696855|gb|BJ957088.1|BJ957088
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37835895|gb|BJ593907.1|BJ593907
EST:     ATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
genomic: ATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGAC-GGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
EST: gi|37834644|gb|BJ592656.1|BJ592656
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|15320319|gb|BI488125.1|BI488125
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37832091|gb|BJ590103.1|BJ590103
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162245980|gb|FC424378.1|FC424378
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67575457|gb|BJ948281.1|BJ948281
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT

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: 31 (upstream exon), 35 (downstream exon)
Score: 15

ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACTATGGAAGATATCCTTGTGGAGCTCAAGAAGCAGATGGCAAGCCCGGCTA




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