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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttaatgattttctacggttctcacaataggcattggacaatatcttgaatggtgcgcggttcaattaacttcagtttttgtgttctttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATGCTTACTCCATCAATTGCAGGTGCTCTCATGGGTATAAGCTCTTTGGGTG

Basic information

species Physcomitrella patens
transcript PP1S121_53V6.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S121_53V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA05G24520.1 (Glycine max), 3'ss of exon 13
--ttctttaatgattttctacggttctcacaataggcattggacaatatcttgaatggtgcgcggttcaattaactt----cagtttttgtgttctttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATGCTTACTCCATCAATTGCAGGTGCTCTCATGGGTATAAGCTCTTTGGGTG
  |  ||   |  || | |  | || |        |||||  | ||||  ||      |  |   ||||| |  | |     | || |     | | ||| | ||||| ||| | ||  | || ||||| |   |  | ||   ||     |   |||| ||||||||||||||||| |||||||||||  | || ||  | || |
aatgtttctgttcttatttgtgattttgg-----agcatttaa-aatactttattatttttgttattcaactgtcatggtgtaattatacctctatctttatacagGTAGGAATTCCAATTGCAGCTGGAGTGTTATTTCCCATAAATGGGACTGTGCTGACTCCATCAATTGCAGGGGCTCTCATGGGGCTGAGTTCCATTGGCG
















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|162173028|gb|FC348653.1|FC348653
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|37851519|gb|BJ609527.1|BJ609527
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162173029|gb|FC348654.1|FC348654
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|37824496|gb|BJ582562.1|BJ582562
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|37828462|gb|BJ586474.1|BJ586474
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162154984|gb|FC331402.1|FC331402
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162246674|gb|FC425267.1|FC425267
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162256486|gb|FC432517.1|FC432517
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162234163|gb|FC410767.1|FC410767
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162163928|gb|FC340150.1|FC340150
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162160038|gb|FC335700.1|FC335700
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGTTTTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|37823296|gb|BJ581362.1|BJ581362
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|22492312|gb|BU052235.1|BU052235
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCCTTCA-CGAACATCAT
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACC-TTCAACGAACATCAT
EST: gi|18339595|gb|BJ171622.1|BJ171622
EST:     CGCTCAGGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162196152|gb|FC373493.1|FC373493
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162214363|gb|FC390082.1|FC390082
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTTTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|18336152|gb|BJ168174.1|BJ168174
EST:     TTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: TTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162180719|gb|FC357804.1|FC357804
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|18333911|gb|BJ165927.1|BJ165927
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|37821393|gb|BJ579459.1|BJ579459
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162163927|gb|FC340149.1|FC340149
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162168675|gb|FC343937.1|FC343937
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
EST: gi|162177315|gb|FC353472.1|FC353472
EST:     CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATT                         GTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG
genomic: CGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATG

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), 34 (downstream exon)
Score: 11

GTTGTTGATGCTCTTGAGTTGAGTCGTTTAACGCTCAAGAAGATAAAACAGAATCTTTGGTGGGCATTCATGTATAATATTgtaagtggat ... ttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATGCTTACTCCATCAATTGCAGGTGCTCTCATGGGTATAAGCTCTTTGGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgaatggtgcgcggttcaattaacttcagtttttgtgttctttttgtccagGTGGGACTCCCTCTCGCTGCTGGTGCTCTGCTACCTTCAACGAACATCATGCTTACTCCATCAATTGCAGGTGCTCTCATGGGTATAAGCTCTTTGGGTG
                     aattaac  putative branch site (score: 11)
                                 tttttgtgttcttttt  putative PPT
                  ttcaattaa  TA-rich tract