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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttttagtttatttatttaaacgtaaattaatatttatactagcttcctttccttttcttttcttttatcttcggtgttttttctatgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTAGACGTTGATATTCTGATCACTGGTCACACTCACCAGTTCAAAGCATACA

Basic information

species Physcomitrella patens
transcript PP1S75_108V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S75_108V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g16550.1 (Oryza sativa), 3'ss of exon 2
catgtttttagtttatttatttaaac---gtaaattaatatttatactagcttcctttccttttcttttcttttatcttcggtgttttttctatgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTAGACGTTGATATTCTGATCACTGGTCACACTCACCAGTTCAAAGCATACA
| | || |||||  ||       |      | | | | | |  |   |    |  |||     | | | ||  | | |||  ||    | | || |||   ||||||| |||||||| |||||||| ||  |||||||||| ||||||||||| ||||| || || ||  |||| || ||||| ||||||||||| || ||||
ctttttgttagtacatgccaaagagtctgatcagtcagtgtcaaacttgagattgttttgcagtgtatcctaatcttttctctgaccatgcaatcatc---agGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTGGACGTGGACATCCTCGTCACAGGGCACACCCACCAGTTCAAGGCGTACA

upper sequence: PP1S75_108V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G068489_T02 (Zea mays), 3'ss of exon 1
catgtttttagtttatttatttaaacgtaaattaatatttatactagcttcctttccttttcttttcttttatcttcggtgttttttctat-gatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTAGACGTTGATATTCTGATCACTGGTCACACTCACCAGTTCAAAGCATACA
||  |  | | ||| |   |     | |  |  | |   |||   |  |   |||  | ||      ||||  ||       |   || || || |  |||||||| |||||||| ||  |||| ||  |||||||||| || |||||||| ||||| || || ||| | || || ||||| ||||||||||| ||||| |
cacatgctaaatttgtgcgtgcggtcattgag-actgactatctgacatatattttgtgttaaacatttttcactaaatctctgcatcgatcgaacaccagGTTGTTCCATGGGGCGACCTGGACTCCCTGGCGATGCTCCAGCGGCAGCTGGACGTGGACATCCTGGTGACCGGGCACACGCACCAGTTCAAGGCATATA
















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|208359218|gb|DC954155.1|DC954155
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208366041|gb|DC951186.1|DC951186
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208346102|gb|DC917055.1|DC917055
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|162252361|gb|FC426169.1|FC426169
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208382188|gb|DC903148.1|DC903148
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208350369|gb|DC906071.1|DC906071
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTCCANCGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|162252360|gb|FC426168.1|FC426168
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGGGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|37827037|gb|BJ585049.1|BJ585049
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208360357|gb|DC949998.1|DC949998
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|162224612|gb|FC400508.1|FC400508
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|37849177|gb|BJ607185.1|BJ607185
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208395383|gb|DC919959.1|DC919959
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208355077|gb|DC922193.1|DC922193
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208391108|gb|DC938138.1|DC938138
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCANCGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208370788|gb|DC936192.1|DC936192
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCANCGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208397474|gb|DC908308.1|DC908308
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
EST: gi|208374342|gb|DC941155.1|DC941155
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGA
EST: gi|162224613|gb|FC400509.1|FC400509
EST:     AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAG                         GTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA
genomic: AGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTA

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: 28 (upstream exon), 34 (downstream exon)
Score: 12

TCAAATTACACGGGGTGAGTATGACGAAGACACCCGCTACCCTGAGACAAAGCAGCTGAATATCGGCGCTTTTAAGCTCGGCATTTGCCACGGCCATCAGgtcttgtctt ... tgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTAGACGTTGATATTCTGATCACTGGTCACACTCACCAGTTCAAAGCATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttcctttccttttcttttcttttatcttcggtgttttttctatgatctgcagGTTGTGCCATGGGGAGATTTGGATTCATTGGCGATGCTTCAACGGCAGCTAGACGTTGATATTCTGATCACTGGTCACACTCACCAGTTCAAAGCATACA
       tttccttttcttttct  CT-rich tract
            ttttcttttcttttat  TA-rich tract