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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG

Basic information

species Physcomitrella patens
transcript PP1S129_53V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 10
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatt-tactgtctgttagttgttgggtatttacttcttgtttaatac-tgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                                      | | | ||    ||    | ||    || || | ||      |       | | | |   || | | || | ||||||||||||||||| |||||||| |||||||||||| | |||||||||||  ||||| | || || |||
-------------------------------------gtaagcatcag--ttgaagcattatttttgtattatccacccataccaaactgtat-ccaattatgttatgcatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 8
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt--atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                    ||  ||    ||   |  ||    |  |  |||||  |  | |   || | ||   |  ||  || |   |||      || | ||| | ||||| ||||||||||| |||||||| |||||||||||||| |||||||| ||  | ||| | || || |||
-------------------gtaagtaactgttaaagaatttttatttttttttggcaggggtacaatattttcccatctttaatgagctgattccaccattctgtaaca-tgcagGTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 8
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttc-ttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                      || ||| | |   ||   |  ||  |  || ||  | | | | |   |  |  |   | ||| | |  || |  | || | ||| | ||||| ||||||||||| |||||||| |||||||||||||| |||||||| ||  | ||| | || || |||
----------------------gtaagtaact---gttacagatttttttttgggggggttacaatattttcccatctttagttagctgattccaccattctgtaaca-tgcagGTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 10
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                    ||   |    ||   |  |||  ||  || |            || |||        |  |||     ||  | || | |||   || ||||||||||||||||| |||||||| |||||||||||| | ||||||| |||  | ||| | || || |||
-------------------gtaagcatcagttgaagcattatttttgtctt------------atctacccataccaaactgt-----atccaattat-gttatgta-tgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCATTGTGTGTGGCATATGATTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA19G08270.1 (Glycine max), 3'ss of exon 9
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctt-tggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactg---cagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                 | ||| | |      | | |||| | |||   ||| ||  | |  |||   |   | |   |  | |     ||    ||     || | | |    ||||||||||||||||||||||||||| |||||  || | |||||||||||  | ||| |||| ||||||
-----------------acttaataacatgcacctttctttctttctgtcttgtgagcttctaaagggatcatatcaaatgtatctaacatagctttgacacttgaaattttctcagATTTGTTGAGATCATGGCTCCTGTATTTTCCAGAGATGCATGGCGTTGTGTGTGGCACATGATACAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
               |||| |||  |    ||  | | |  || |  |   |||||  ||     | || |    | |   ||   | | ||   | |  || || | |||||||| || ||||||||||||||||| |||||| |||| || ||||| ||| | ||| |  | || |||
---------------gtatgtag--aagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv14s0066g00310.t01 (Vitis vinifera), 3'ss of exon 8
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
|||      ||   |  |||||  ||  ||    | |   |  ||   |  |  |    ||   | |    ||   ||  | ||   |  ||| | |||    |||| ||||| |||||||||||||||||| |||||||||| ||||| |||||||||||  | ||| | || || |||
gtatgtgcacagatttaatttaagtacagaacattttgaaaatttgtactgtaaggaactgttttatggattcaaataaatctttattgattattactta---aata-tgcagCTTTGTTGAGATCATGGCTACTGTGTTTTCTCGAAATGCATGGCGTTGTGTTTGGCATATGATTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
--gtaataag--tcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
   | | |||  |  | | ||| |   ||  |  ||  ||| ||   | || |   ||   | |     | ||  |   ||||        | |||   || |  |||   | ||||| ||||||||||||||||||||||| |||||  || | |||||||| ||  | ||| | ||  | |||
gtatgaaaagctttgagcagtact--attgttattttttgtgttcattcccactcctgcatggt----ctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 1
gtaataagtcaacctgtatttagt-tagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
    || |  || || |    | |    |  ||  | | |    |   |||       |       | ||  |   ||||        | |||   ||    |||   | ||||| ||||||||||||||||||||||| |||||  || | |||||||| ||  | ||| | ||  | |||
---gtatgaaaagctttgagcaatactattgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
        |  | | ||| |  |||  |  ||  | | ||   | || |   ||   | |     | ||  |   ||||        | |||   ||    |||   | ||||| ||||||||||||||||||||||| |||||  || | |||||||| ||  | ||| | ||  | |||
--------ttgagcagtact--gttgttattttttctgttcattcccactcctgcatggt----ctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv05s0077g00080.t01 (Vitis vinifera), 3'ss of exon 5
gtaataagtcaacctgtatttagt-tagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
    || |  || || |    |||   ||  ||  | | |    |   |||       |       | ||  |   ||||        | |||   ||    |||   | ||||| ||||||||||||||||||||||| |||||  || | ||||| || ||  | ||| | ||  | |||
---gtatgaaaagctttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGACGGTGTGTGTGGCATATGCTTCAG

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtt--taatactg-cagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG---------------------------------
                                                         ||     ||  || ||  || |   |  | | | || |||||  |  |  | ||| ||||||||| |||||||||||||| ||||||||  | || || ||| | ||| | ||| | || |||||                                  
---------------------------------------------------------gtaagtcttggctttcacttggacat-agatttctatttcttagtggtgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC

upper sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ09147 (Selaginella moellendorffii), 3'ss of exon 6
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttctt---gtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG---------------------------------
                                                         ||     ||  || ||  || |   |  | | | || |||||   |||   |   |||||||||| |||||||||||||| ||||||||  | || || ||| | ||| | ||| | || |||||                                  
---------------------------------------------------------gtaagtcttggctttcacttggacat-agatttctatttcttagtgttgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC

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|162181747|gb|FC357346.1|FC357346
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37844061|gb|BJ602069.1|BJ602069
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162268144|gb|FC443822.1|FC443822
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162268143|gb|FC443821.1|FC443821
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37841807|gb|BJ599815.1|BJ599815
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37849671|gb|BJ607679.1|BJ607679
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162198683|gb|FC373464.1|FC373464
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162165626|gb|FC341465.1|FC341465
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|208371453|gb|DC955789.1|DC955789
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162165627|gb|FC341466.1|FC341466
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37827443|gb|BJ585455.1|BJ585455
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162198682|gb|FC373463.1|FC373463
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT

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), 32 (downstream exon)
Score: 14

GGAAGCAGTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
                                         gtttaat  putative branch site (score: 14)
                                       ttgtttaata  TA-rich tract