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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgactctatgtatattgcataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA

Basic information

species Physcomitrella patens
transcript PP1S212_85V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
gcgactctatgtatattgc--ataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA------------
              |||||  ||   |      | |     |  |  || | |   | |   |   | |  | |    | ||||| |  | |   || |||||||||||| || || ||||| ||| | ||||| || || || |||||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||            
--------------attgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
gcgactctatgtatattgcataat-acctgtcgaatgacctgc----tggtttctgccttgttgtcaaa-----tatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
           | | || ||| ||  ||  | ||||||  |||    |  ||| |  |  ||| ||  |     | |  | |    | ||||| |  | |   || |||||||||||| || || ||||| ||| | ||||| || || || |||||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||
----------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
gcgactctatgtatattgcataatacctgtcgaatgacctgctggtttctgccttgttgtcaa------atatgtcgtggatgcctcacagtgtta-------agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
           ||  ||| | | | | ||    ||  | ||||  |||||   |||   || |      || | || |   | |     | | | |          ||   |||||||||| ||||||||||| ||  ||||||||||||| || ||||||||||| || || ||||| || |||| ||| |||||||| ||||| ||||| |
-----------taatttgaa-agtgcatgcaatattgc-tgctcctttctattttgccatctaaaaggcatttctccttattactatttactataactttgttgatttgctagGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------gcgactctatgtatattgcata-atacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtg-gat--gcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
                  ||  |||  | |  |||  ||   ||  ||| |||| | || |  ||||     | ||  |   || |   ||| |||    || |   | ||    |  | ||||||| || || ||||| || ||||| ||||||||||| || ||||||||||| || || |||||| | |||| ||| ||||| || |||||||| ||||
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttc--gtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------gcgactctatgtatattg-cataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
                                         | || |  ||  ||| ||   |  ||   |  |    |  ||  | | |     || |  ||||| |||||   |||||     | ||||    ||   ||||||| || || ||||| || ||||| ||||||||||| || ||||||||||| ||  | |||||| | |||| ||| |||||||| || ||||| || |
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttat-atcaaagatgtctctgatgct----aatgtt----ttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------gcgactctatgtatattg-cataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA------------
                                         | || |  ||  ||| ||   |  ||   |  |    |  ||  | | |     || |  ||||| |||||   |||||     | ||||    ||   ||||||| || || ||||| || ||||| ||||||||||| || ||||||||||| ||  | |||||| | |||| ||| |||||||| || ||||| || |            
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttat-atcaaagatgtctctgatgct----aatgtt----ttggtaggtgattacaaagTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATATCATGAAATTGG

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 1
gcgactctatgta-tattgcataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatg---tcgtggatgcctcacagtgttaagcttt-tcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
     | ||  ||  |||  | | |   |||  ||     |  |    | |   || |     | ||||   | |||  ||  ||  |       |||||   ||||||| || || ||||||||||| ||||||||||| || |||||||||||| |||| || |||||||| |||| ||| ||||| || || || |||||||
-----tttagatagcattataaatttagtgtttaagatttttataaagtgttgtttttccgacagtatggaattgtgtctgtttctgatccagctgctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTATTCTTACCTAAACAACCGAAAGAAAGTGACAGCTGTGCACAAAGCCAACA

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
gcgactctatgtatattgcataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
                                  |   |   |   |||| |  || | |    |  | ||     ||  |      |   ||    |||||||| || || || ||||||||||| ||||| |||||||| |||||||| || || || |||||| | ||||| || || || || || ||||||||||
---------------------------------gtactccaatttcttctcctctgcttt--gctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

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|67698118|gb|BJ958351.1|BJ958351
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|208356872|gb|DC926883.1|DC926883
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|67692443|gb|BJ952676.1|BJ952676
EST:     TCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: TCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|208373524|gb|DC941093.1|DC941093
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|162265636|gb|FC441092.1|FC441092
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT

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: 27 (upstream exon), 31 (downstream exon)
Score: 6

CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
                               gcctcac  putative branch site (score: 6)
                                               cttttc  putative PPT
              tcaaatat  TA-rich tract