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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgttgttacgtccctcatatttcataatacagtactaatggtcgcaattctgagcattccatgacttcatgcatttgcgaattgtag

Basic information

species Physcomitrella patens
transcript PP1S204_49V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os06g36160.1 (Oryza sativa), 5'ss of exon 2
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgttgttacgtccctcatatttcataatacagtactaatggtcgcaattctgagcattc-catgacttcatgcatttgcgaattgtag
| | ||||| || ||||| ||||||||||| ||||| ||||||||||| |||    ||||| | ||||| || |||||||| ||||||||||| || |||||| |      ||| | |  || |   | |||| |  |   | ||   |||    | |   |    |     || |||  ||    ||| | | | | |  |  | ||          
CCGCACCCACTTCGGAGGCGGCAAGTCCACCGGATTCGGCCTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacg------cacgcatcgctcagaactttgt-gccatcactct-gcattctgaatttgggattgagctagcggaatggtggttgttcgcctcagtgctcggttgtg----------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgttgttacgtccctcata-tttcataatacagtactaatggtcgcaattctgagcattccatgacttcatgcatttgcgaattgtag
| | ||||| || ||||| ||||||||||| ||||| || |||||||| |||    ||||| | ||||| || |||||||| ||||||||||| || |||||| | |  ||   |   |   | ||  || |   |   |  | | ||| |||  |   |  ||  |  |   |  || ||||| || || |  ||| |  |  |             
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctct--cttgtctcgttgatctcgccct---gctcttgatagtttagtttaatcgtgatgctatgctgaaatctgaacaatctagtactactagagt-------------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G091383_T01 (Zea mays), 5'ss of exon 2
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgtt-gttacgtccctcatatttcataatacagtac-taatggtcgcaattc--tgagcattccatgacttcatgcatttgcgaattgtag
| | ||||| || ||||| |||||||| || ||||| || |||||||| |||   |||||||| ||||| || | |||||| |||||||||||||| |||||||| || ||   | | | | | |   ||   | || |      |||||  ||   ||   | |  || ||   |  || |  |||    || | |  |                     
CCGCACCCACTTCGGAGGCGGCAAGTCTACCGGATTCGGTCTCATCTACGACAACGTCGACTCAGCCAAGAAGTTCGAGCCCAAGTACAGGCTTATCAGGgtatgcgtctcttgctcctcccgtttttctcactcgtaattggattcataggtctccatgttgaatatactgcctggtatacgctgaaagctcaaagctt---------------------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA20G37190.1 (Glycine max), 5'ss of exon 3
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgttgttacgtccctcatatttcataatacagtactaatggtcgcaattc--tgagcattccatgacttcatgcatttgcgaattgtag
  | || || ||||| ||||||||||||||||| |||||  | |||||||| || || ||   |||||| || ||||||||||||||||||||||| |||||  ||  ||  |  | || |||   |  || |  |||      |     ||  | | |  |  ||  |  |   ||||    | ||  |  || | |  ||                 
TCGAACTCATTTTGGTGGTGGCAAGTCCACTGGGTTTGGTTTGATCTATGATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatttaaatcttt-ctgtgtcaattatgattataatttttcccctttgttaaaatgc-cttttttttttaattagacgggctgtttataaata-ata----------------

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|162207611|gb|FC384064.1|FC384064
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162207612|gb|FC384065.1|FC384065
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162264253|gb|FC441355.1|FC441355
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162211993|gb|FC388455.1|FC388455
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162231344|gb|FC406767.1|FC406767
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162184761|gb|FC361063.1|FC361063
EST:     CTCTGTCGACTCTGCCNNNNNNNTACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: CTCTGTCGACTCTGCCAAAAAA-TACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|67722912|gb|BJ973171.1|BJ973171
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162184143|gb|FC358889.1|FC358889
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162211994|gb|FC388456.1|FC388456
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162264252|gb|FC441354.1|FC441354
EST:     ACTCTGTCGACTTTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|7147798|gb|AW509720.1|AW509720
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|67728029|gb|BJ978288.1|BJ978288
EST:     ACTCTGTNGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162184760|gb|FC361062.1|FC361062
EST:     CTCTGTCGACTCTGCCNNNNNNNTACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: CTCTGTCGACTCTGCCAAAAAA-TACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|162252337|gb|FC427276.1|FC427276
EST:     CTCTGTCGACTCTGCCNNNNNNNTACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: CTCTGTCGACTCTGCCAAAAAA-TACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
EST: gi|67722063|gb|BJ972322.1|BJ972322
EST:     ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGG                         AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC
genomic: ACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGC

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), 33 (downstream exon)
Score: 81

CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgttt ... cgaattgtagAATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG




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