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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttctatttgttgggttgctattagtaatccccacgccatgtgggatctgcggaagtggtctgtgagggtttacctatcaaaatggtttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA

Basic information

species Physcomitrella patens
transcript PP1S34_445V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 3
-tgccttcta-tttgttgggttgctattagtaatccccacgccatgtgggatctgcggaagtggtctgtgagggtttacctatcaaaatggtttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA
 | | ||  | |||  || | | || | |   ||    |  | |    | ||||||         |  | | |  ||   | ||    | | ||   |||||||||| || |||||||||||||||||||| || || |||      || |  | |||||| || || |||||||| || ||| |    || || || ||||
gtacatttcactttactgagat-ctttcaaagatgattat-caacaatgtatctgc-----cttccattaatgacttggttttct---ttggtttaatgcagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGTGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 2
tgccttctatttg--ttgggttgctattagtaatccccacgccatgtgggatct-gcggaagtggtctgtgagggtttacct-atcaaaatggtttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA
     | || |||  ||| || |  |||| ||| |   |   |||| ||  | |      |||      ||| |  ||| ||        |   |      |||||    || |||||||||||||||||||| |||||||||  |   || || |  ||||| || || ||||| || || ||| |    || || || ||||
----gtatacttgaattgagtcgagatta-taa-caagatagcatgaggattttcatcctagttagtactgatgccttatctcgctcttgttactgaacaacagGATAGCACCTACAAGTACTTTGAGATCATCCTGGTTGATGTGGCCCACACTGCCATCCGCAACGACCCAAGAATCAACTGGCTATGCAATCCTGTGCACA

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G034794_T03 (Zea mays), 3'ss of exon 1
tgccttctatttgttgggttgctattagtaat-ccccacgccatgtgggatctgcggaagtggtctgtgagggtttacctatcaaaatggtttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA
    |    ||  ||| ||||   |||  ||     || |  |  |   |||   |  |||  |         | |  || |     |   |      |||||    || ||||||||||||||||||||||| ||||||  |   || ||    ||||| || ||||||||||| || ||| |    || || || ||||
---gtatgcttaattgagttgagcttaacaagatatcatgagaattttcatccttgtcagtactgatgccacatctggctcttg---ttactggacaacagGATAGCACCTACAAGTACTTTGAGATCATTCTTGTTGATGTGGCCCACACTACCATCCGCAATGATCCAAGGATCAACTGGCTATGCAATCCTGTGCACA

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|208347591|gb|DC925534.1|DC925534
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162181735|gb|FC358765.1|FC358765
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162215478|gb|FC390543.1|FC390543
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162211655|gb|FC387943.1|FC387943
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67575228|gb|BJ948052.1|BJ948052
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162215477|gb|FC390542.1|FC390542
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|18370179|gb|BJ201781.1|BJ201781
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67709455|gb|BJ965271.1|BJ965271
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|208346895|gb|DC905439.1|DC905439
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67698687|gb|BJ958920.1|BJ958920
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|100363460|gb|BY966400.1|BY966400
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|37826795|gb|BJ584807.1|BJ584807
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|18340479|gb|BJ172507.1|BJ172507
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67723886|gb|BJ974145.1|BJ974145
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|208379859|gb|DC911744.1|DC911744
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162268392|gb|FC444161.1|FC444161
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|208346559|gb|DC916825.1|DC916825
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|18347722|gb|BJ179769.1|BJ179769
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162262360|gb|FC437687.1|FC437687
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67723423|gb|BJ973682.1|BJ973682
EST:     CCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: CCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162211656|gb|FC387944.1|FC387944
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162181734|gb|FC358764.1|FC358764
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67709347|gb|BJ965163.1|BJ965163
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|67709809|gb|BJ965625.1|BJ965625
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|37851003|gb|BJ609011.1|BJ609011
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|208382335|gb|DC919323.1|DC919323
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|208376710|gb|DC902919.1|DC902919
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162201995|gb|FC377201.1|FC377201
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
EST: gi|162201996|gb|FC377202.1|FC377202
EST:     GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAG                         GACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA
genomic: GAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACA

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: 32 (upstream exon), 35 (downstream exon)
Score: 10

ACAGCTTAAGTTCCAGCGTAACTTGCGATCAGTAGCTGAGGAGCGGGCAGGAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccat ... ttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatctgcggaagtggtctgtgagggtttacctatcaaaatggtttcggtgcagGACTCTACATACAAGTACTTTGAGATCATTCTGGTTGATCCGCAACATACAGTTATCCGTAAGGATCCAAGGATTAATTGGATTGTGAACCCCGTTCACA
                                 tatcaaaat  TA-rich tract