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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat...

Basic information

species Physcomitrella patens
transcript PP1S168_28V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcata---cttatccccgtatctttgacatcgccttg--ttgaaatcgaacaattat-
 || || |||||||||||||||||||| || ||||| |||||| | ||||| |||||||| || || ||||||||||| || |||||||||||||||||||||      |  |  ||| |   ||||||  |||        ||||||| | |    |  | |  ||||  ||  || |  || |  ||        ||  | || 
AAACGATATTCACATTGACATCATGGATTATATCTCACCTGCTACTTGTGCCGATGTTGCTTTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgta------gggttctttctcaagcttcagcttttgcaaatgcttgttttacaagattctttcatgtattatttgcagctgctagattttcttcttcactgtgatc

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattct---tttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 ||||| |||||||||||||||||||| || ||||| || ||  | || ||||||||| | || || ||||||||||| || |||||||||||||||||||||  ||   ||||    |||| | |  |   ||  | | | |   ||||   ||  |   | |   |  |||   |     |  |||   ||      ||| 
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgt--tcatctgttta-

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G392003_T01 (Zea mays), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttg--ttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 ||||||||||||||||| || ||||| |||||||| |||||| ||||||||||||||||||| || ||||||||||| || |||||||||||||| ||||||     |   |  | ||  ||||  ||    ||||||  |   || | |  |  || || | |   || |  | |  |  |  |   ||  |    | | 
AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacctcttgtctgattttttgtttgtttttcatgatggtttctgtagtttttgtcgcaggcactatcgc-ttacacttctaccatataggtgtaa-

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G011101_T01 (Zea mays), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgct-tcaagtttcattctctcttgtttcatacttatcc-ccgtatctttgacatcgccttgttgaaatcgaacaattat
 ||||| |||||||| ||||||||||| |||||||| |||||| | |||||||||||| | || || ||||||||||| || ||||| |||||||| |||||| | ||   |   | |   ||||  |   |    |||   |   |    ||  |  |   | ||| | |        |   |||  |  | | ||  || 
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaac-atgcttctctgtacgttgcagttgtgaaatatttgtttcagcaaaatgttcttaaactgtagcctcctttatactcagttttatactagcacata-

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgt-atctttgacatcgc--cttgttgaaatcgaacaattat-
 ||||| |||||||| ||||||||||| |||||||| |||||| | ||||| |||||| | || || ||||||||||| || ||||| |||||||| ||||||   ||    |  | |||     | ||  | | |      |||      || |   |    | |||  ||  ||     | |||     |  || ||     
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgta---atatgcttctctgtac-attgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G23780.1 (Glycine max), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgctt--caagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat-
 ||||| || || |||||||||||||||||||| |||||||| || ||||||||||| |||||  | |  |||||||||||||||||||||||||||||||||| | ||  | ||  |  | |  ||  | |  ||  |   |    | |  | |  |||     || ||||    | |||     | || |  ||  | || 
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCTGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatatctctttcctccttctctcattggctatgtttttaaccaaagggtaaaaaaatatggtgctaccttt--tcttgcccaaa-gcaaccccactttcatt

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G00610.1 (Glycine max), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgctt--caagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat-
 ||||| || || |||||||||||||||||||| |||||||| || ||||| ||||| |||||  | |  |||||||||||||||||||||||||||||||||| | ||  | || ||  |    ||  | |  ||  |  ||    | |  | |  |||     |||||||    | || |    | ||    ||  | || 
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctctttcctctttctcccattggctatgtttttaatcaaaaggtaaaaaaatatggtgctatcttt--tcttgc-tcaaagcaactccactttcatt

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgta-tctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 |||||||| |||||||| ||||||||||| ||||| ||||||   ||| | || ||||| ||  | |  |||||||| ||||| || ||||||||||||||| | ||| ||  | ||| | | | |  |  ||   |||     | | |   | ||            ||    | |  || || |  ||          
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaaccttt-tatagttgtaccttcttttcgtatgtttgttggagtttggtataaccaattcctgttgtattctttatgtcag--------

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 5'ss of exon 3
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgta-tctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgac--atcgccttgttgaaatcgaacaattat
 || ||||| |||||||| ||||||||||| ||||| ||||||   ||  | || ||||| ||  | |  |||||||| |||||||| ||||||||||||||| | || |||  | |||     |  | |  ||   |  |   ||||||  ||  | |     || |  |  |   | |  || || |  ||          
TAACGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGCTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaatttaccgaaaccttttaaaagtattaccttctttgtttgtttgtttgttagattttggtataaccattgcctgttgtattattcatgtcag--------

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgta----tctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 |||||||| || ||||| || ||||| ||||| ||||| || || ||||||||||| |||||| | | ||||||||||||||||||||||||||||||||||    |||    ||  ||   | ||  ||  | |   ||  | | ||| |   |   | |   |   | |   | |  || ||| | | || ||||| | | 
CAATGACATCCATATTGATATAATGGATTACATTTCTCCGGCATCCTGTGCTGATGTGGCATTTAGAACCATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtacgtctctcataatatttgcttcttaatttcaatactatatt-tattgatcggtctctttgagcaagtttcccagactgctttgataacat-gaaca-tca-

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccc-cgtatctttgacatcgccttgttgaaatcgaaca--attat-----
 |||||||||||||||||||||||||||||||| |||||||||   ||| ||||||| || ||  | |  |||||||| |||||||| |||||||||||||||       ||  | | | | | |||| |   |  | |    | ||  ||| || |||    |  |  |||| |||   ||||| | | |  |||   ||||     
CAATGACATTCACATTGACATCATGGACTACATATCTCCTGCTGTTTGTACTGATGTGGCCTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgta------aatcatctagctgtccttccatgattttcccaaatggtaacat-ctgatctaatgggtacttga-atctttttgtttataccttacatagttatttttg

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ07199 (Selaginella moellendorffii), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattct---ctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 || ||||| |||||||||||||||||||||||||| || || || ||  | || ||||| ||| | ||||||||||| |||||||| ||||| |||||||||        || || |   ||  ||   | |  ||  |   | || || |  | ||| | |                                        
CAACGACATCCACATTGACATCATGGACTACATCTCGCCGGCCTCGTGCCCCGACGTTGCCTTTAGGAACATGTGGGCCGAGTTTGAATGGGAGAACAAGgtacgcgagagtttttctcccttttttttcgatcgatggtacgcactcgtgttcttcttgtgcag--------------------------------------

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ09162 (Selaginella moellendorffii), 5'ss of exon 2
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat
 || ||||| |||||||||||||||||||||||||| || || || ||  | || ||||| ||| | ||||||||||| |||||||| ||||| |||||||||      || | |||    ||| ||    ||||  ||  |  |    || |||  |   | |  || ||                             
CAACGACATCCACATTGACATCATGGACTACATCTCGCCGGCCTCGTGCCCCGACGTTGCCTTTAGGAACATGTGGGCCGAGTTTGAATGGGAGAACAAGgtacgcga-gagtttttctccttgtttt---tttcgatcgatggtagcacacactcgtgttc-ttcctgtgcag--------------------------

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|162168142|gb|FC343832.1|FC343832
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37847066|gb|BJ605074.1|BJ605074
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCNCCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37837708|gb|BJ595716.1|BJ595716
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37850559|gb|BJ608567.1|BJ608567
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|162174369|gb|FC350440.1|FC350440
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37842166|gb|BJ600174.1|BJ600174
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37827266|gb|BJ585278.1|BJ585278
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|18338077|gb|BJ170101.1|BJ170101
EST:     CTGATGTTGCATTTNGCAACATGTGGGCTGAGTNTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37845300|gb|BJ603308.1|BJ603308
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|37827044|gb|BJ585056.1|BJ585056
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
EST: gi|162167676|gb|FC343990.1|FC343990
EST:     CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT
genomic: CTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcg ... gcttttccagGTAGCAATAAATACCACCATTCAAGACGTTCGGGAGTTCTTGCAGCATATT