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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S211_21V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
----acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
      || ||   |||  || || |  |        ||  ||     ||| || |   |   | |||||| |||   ||     || ||     | ||  ||||||| || ||||| ||||||||||| |||||||| || |||||  |||||||||||||  |||| |||||||| |||||| | |  |||
ctctgtga-ttgtgaaccaaaagagagatgagatacagtttttatgcataa-atataatggcca-ttaagaataacagcttgctgct-ggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 4
----acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG-----------
      || ||   |||  || || |  |        ||  ||     ||| || |   |   | |||||| |||   ||     || ||     | ||  ||||||| || ||||| ||||||||||| |||||||| || |||||  |||||||||||||  |||| |||||||| |||||| | |  |||           
ctctgtga-ttgtgaaccaaaagagagatgagatacagtttttatgcataa-atataatggcca-ttaagaataacagcttgctgct-ggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGGTTATTATATA

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
acgagttcccaacttaacgaaaactatctctgtgtacttga-atttaacatgttgcgtttaattaagactaatttctgcaaacttggctt-cgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
  | ||||   | ||   |   ||   |  | | |  || | | |||||||||    ||| |       ||  || |  |   |||  |  | | ||  |||||||  | |||||||| |||||||| || |||||||| |||||| | || ||||| ||| ||||||||||||| || ||| | |  |||
-tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtca-atttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 4
---acgagttcccaactta-acgaaaact--atctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
       ||   ||| ||    | |  ||  ||   |||| | |  | ||||   | | |  | | ||||| |  |||| ||||    ||    | || |   |||||||||| |||||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  |||
atggaacgtaaacaatttttgtggagccttgatggatgtggattacagtttactgtatggtttgtgattaaca--aattcctgctg--ttactcttgtctg--cagATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
acgagttcccaacttaacgaaaactatctctgtgta--cttgaatttaacatgttgc-gtttaat-taagactaatttctgcaaacttg-----gcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
          ||   || |||||| || |  |||||  |||||     |     | | ||||| | || || |  |   |     |||      || || | ||  |||||||| | |||||||| ||||| ||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  |||
---------gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatg---ttgcgtttaattaa-gactaatttctgcaaacttggcttcgtt-tcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG-----------
     ||   |  | |   || ||||   |    ||  |||  |   |||    ||   |   || || ||   ||| | | ||   | | ||| ||  |  |||||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||           
-----tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatg---ttgcgtttaattaa-gactaatttctgcaaacttggcttcgtt-tcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
     ||   |  | |   || ||||   |    ||  |||  |   |||    ||   |   || || ||   ||| | | ||   | | ||| ||  |  |||||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||
-----tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
---acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG-----------
   |||| |   |  ||| |        || |||    | ||   |||      |     |    ||   ||| |  ||    | |   |  | |  |  ||||||| || |||||||| ||||| ||||| ||||| || ||||||||||| ||||||||  | || ||| |||| || ||  | |  |||           
tgtacgactaatc--cttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatatt-ctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 5
---acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
   |||| |   |  ||| |        || |||    | ||   |||      |     |    ||   ||| |  ||    | |   |  | |  |  ||||||| || |||||||| ||||| ||||| ||||| || ||||||||||| ||||||||  | || ||| |||| || ||  | |  |||
tgtacgactaatc--cttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatatt-ctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
acgagttccca-acttaacgaaaactatctctg----tgtacttgaatttaacatgttgcgtttaattaagactaatttc-tgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
    ||| | | || |||  |  | |||  | |      |  | | |   |     ||  | |||  |  |  |||| |    ||  ||    ||| |||    ||||||||| |||||||| ||||| ||||||||||| ||||||||  |||||||||||||||| || ||| | || |||||  | |  |||
----gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggatta--tgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
acgagttcccaacttaacgaaaactat-ctctgtgtacttgaatttaacatgttgc-gtttaattaagactaattt--ctgcaaacttggct--tcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
      ||  |||  | |  ||| ||| |      ||||   |||||  |  | || ||  |||  |   | ||    ||| |||  ||  |  | | || | |||||||||| |||||||| ||||||||||||||||| |||| |||  ||||||||||||| || || ||| | || |||||| | |  |||
------tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
--acgagttcccaacttaacgaaaact---atctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
    |  ||   | |  |  | | |||   || || ||    |   |||||||||    |   |    ||||  | | |||| |   |  |  || |     |||||||| | ||||| || ||||| ||||| ||||| ||||||||||||||||| |||||||| |||||| | || || || ||||  |||
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctgg--aaga--agtatctg-atgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
-acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaac--atgttgcgtttaatt--aagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
     |   |||| |     |     ||     |||   | ||  ||||  ||||  | || |||   ||   | || | |    |||    |  | |   | ||||||| | ||||| |||||||| ||||| ||||| || |||||||||||||||||||| || |||||| | || || ||||||||||||
tttatggatccaaatatgttagtttgattatgatgt--ctaaaactaacttatgtacctttcaatctgaaattttatatttattgactca--tgtgatgtgc-agATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaaga--ctaatttctgcaaacttggct---tcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
    ||||  |  | ||    |  ||| | | |  |||     |       |     |  || || |  || |  |||   | | | |||   | ||||   |||||||||| ||||| || ||||| ||||| ||||| || ||||| ||||| |||||||| || |||||||| || || ||||||||||||
---ggttcttatttcaatccca-ttattt-tatcaactgattctctgtggttgattgtccatcaacacactgacatctaatatcatagcttatttgttttcacagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
------acgagttcccaacttaacgaaaactatctctgtgtacttg-aatttaacatgttgcgt--ttaattaagacta---atttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
           |  |   ||          ||  ||| |  |   |  ||  | | || ||  |  |  | | | |||    |||||| |     ||  | | | || ||||||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctc-ccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
acgagttcccaacttaacgaaaactatctctgtgta-cttgaatttaacatgttgcgt--ttaattaagactaatttctgcaaacttg-gcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
                  |||   |   ||| |  | | |  ||  | | || ||  |  || | | | |||  |   | |     || |  |  ||   ||||||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||
----------------gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttcttttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG

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|208391186|gb|DC938160.1|DC938160
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|162160478|gb|FC336868.1|FC336868
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|208393338|gb|DC942464.1|DC942464
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|208365856|gb|DC955459.1|DC955459
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|67579063|gb|BJ951214.1|BJ951214
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|162221639|gb|FC397864.1|FC397864
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|208366092|gb|DC951209.1|DC951209
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
EST: gi|162160477|gb|FC336867.1|FC336867
EST:     CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTG                         ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA
genomic: CGTGCCTCCTTTGCACCCGCACATCTACAGCAATGGCCATATATGTCTTGgtgagttcta ... gtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
                    gactaat  putative branch site (score: 2)
                                         cttcgtttc  putative PPT
           tttaattaagactaat  TA-rich tract