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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT

Basic information

species Physcomitrella patens
transcript PP1S99_129V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 5
----------------------------taatggagctcccg---agagcttgtaaatc-tagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
                            |  ||||     ||     | |||  ||||  |  |  | | |     || |  |    |   | |  ||  ||  |    |   | || | ||       ||||  | || || ||   ||| |||| ||| ||||||||||| ||||||||| | ||||| || |||||||| || ||||| ||||| || |||||||||||
gtaatcattgtttatcacaaatatttgatgttggaatggtcgtttgtaccttagaaatagtgcaggcactactcatatatctgtccaattttgacactaatgacactgatctgggtttaattcctttaccagGCACACCATTCCCGCCAAACTTCAAGGAGGTTGTAAAGACAATTTTCAAGCGCTTGTTTCGTGTTTATGCCCACATATATCACTCCCATTTTCAGAAGAT

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os08g06610.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
                                       | |||  |  ||  |||  | ||  |   |  |     | |||  || ||   |||     |     |   | |    |  | || |||        ||||  | || || ||   ||| |||| ||| ||||||||||| ||||||||| | ||||| || |||||||| || ||||| |||||    |||||||||||
gtaatcattgtttgtcacaaacatttgatgttggaatggtcatgt-gtaccttagaaatagtgcaggcactactcatatatttgtccaattttgaca--caactcatgacactgatatgggtttaattcctttac-cagGCACACCATTCCCGCCAAACTTCAAGGAGGTTGTAAAGACAATTTTCAAGCGCTTGTTTCGTGTTTATGCCCACATATATCACTCCAGTTTTCAGAAGAT

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G34550.1 (Glycine max), 3'ss of exon 5
taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttg-taatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
   || || |    |    ||       || |   ||  |  |||| ||  ||| |  ||| |  ||||| ||  ||   |      ||       || |||  | || ||||||   || || | ||||||||| ||||| || |||||| | |||||||| || ||||| || |||||||| |||||||||||||| ||
--gtgaagatttttaatattttctttcttaaaggttcttagatgatatagtcattatcattttcattttggtaccataacctataaaatca-----tgtagGTTCACCATTTCCTCCCAACTTTAAGGAAGTTGTGAAGACAATATTCAAGCGGTTGTTCCGTGTATATGCTCACATATACCATTCTCACTTTCAGAAAAT

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA01G35130.2 (Glycine max), 3'ss of exon 5
taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttg-taatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
   |  || |    | |  || |   |  |  ||    | || ||| |   ||| |  ||| |  ||||| ||  ||   |      ||       || |||  | || ||||||   || || | ||||||||| ||||| || |||||| | |||||||| || ||||| || |||||||| |||||||||||||| ||
--gtaaagattttaatattttctttcttaaagattcttagat-gatatggtcatcatcattttcattttggtaccataacctataaaatca-----tgtagGTTCACCATTTCCTCCCAACTTTAAGGAAGTTGTGAAGACAATATTCAAGCGGTTGTTCCGTGTATATGCTCACATATACCATTCTCACTTTCAGAAAAT

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
                                     |    || |    |  || |    | |    | ||| |   |   |||   ||    ||||||| || |||||||||   || |||| ||| ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||| || || ||||||||
-----------------------------------gtacgtctgtttggtgattgggagaaagtggcatctaaaaaccttgtcttctctt----ctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ29107 (Selaginella moellendorffii), 3'ss of exon 5
taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
                                     |    || |    |  || |    | |    | ||| |   |   |||   ||    ||||||| || |||||||||   || |||| ||| ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||| || || ||||||||
-----------------------------------gtacgtctgtttggtgattgggagaaagtggcatctaa-agacttgtcttatctt----ctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT

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|162170893|gb|FC346584.1|FC346584
EST:     TGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACNNNNNNNTAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAG
genomic: TGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCAC-AAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAG
EST: gi|37841636|gb|BJ599644.1|BJ599644
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162246776|gb|FC423874.1|FC423874
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162230785|gb|FC406416.1|FC406416
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162240619|gb|FC419162.1|FC419162
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67697574|gb|BJ957807.1|BJ957807
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67575885|gb|BJ948709.1|BJ948709
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162215256|gb|FC391648.1|FC391648
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|7584173|gb|AW700071.1|AW700071
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162170894|gb|FC346585.1|FC346585
EST:     TGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACNNNNNNNTAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAG
genomic: TGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAA-TAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAG
EST: gi|162266887|gb|FC443001.1|FC443001
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67726815|gb|BJ977074.1|BJ977074
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|37844367|gb|BJ602375.1|BJ602375
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162230786|gb|FC406417.1|FC406417
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162240620|gb|FC419163.1|FC419163
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67694230|gb|BJ954463.1|BJ954463
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162215557|gb|FC391649.1|FC391649
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|7207622|gb|AW561562.1|AW561562
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67694212|gb|BJ954445.1|BJ954445
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|37845448|gb|BJ603456.1|BJ603456
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|18364712|gb|BJ196785.1|BJ196785
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCT
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCT
EST: gi|162266886|gb|FC443000.1|FC443000
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|67693080|gb|BJ953313.1|BJ953313
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
EST: gi|162246775|gb|FC423873.1|FC423873
EST:     CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAG                         GGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA
genomic: CTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGA

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), 23 (downstream exon)
Score: 4

AAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAGCTTGACGATGAAGCCATATTTCCACAAAAAATAGgtctacctac ... ggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT
                                    gcttgat  putative branch site (score: 4)
             attattcttttgtaat  TA-rich tract