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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG

Basic information

species Physcomitrella patens
transcript PP1S276_96V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctg-attccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
             |   |   |   | | |  || ||     ||| |  | ||   |       |  |  || | | ||      ||| | |  |   ||||||||||| || |||||||| || ||||| ||||||||||||||||| ||  | || ||||| ||||| || || ||||||||| |||| |  || ||  
-------------gtcaaaggaaactgtttttagatccatgaattataacttgtttcttg----tattgtcattctaaattgtttgaattttacacaacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 4
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
             | |     | | |   ||    | ||  || || |       | |     | ||||     |     |      |   |  || ||||||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||  | ||||| || ||||| ||||| ||||| || || ||||  |||    
-------------gttggtgaatgttgattgttactttg--cagttctctgcagtcta-----tggatctttgaaagtgtctgtgttacatttgttgcagGTTATCATCGTGACCAGCTCGTTGATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCTAATGCAATAAGAGTTCTTTGCCGCATCATTGACTCAA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
agcttgacatagagattagata--cgatatgtgaaggtctgaaca-ttttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
               ||| |||   ||| | |  || |    ||| | ||||     ||    |   | || | || ||     | |   |   |  |   |||| ||||| || |||||||| ||||||||||| ||||| |||||||||||  | || ||||| ||||| || || ||||| ||| |||| |  || ||| 
--------------gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
agcttgacatagagattagatacgatatgtgaaggtc-tgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
               || |  || ||  ||        ||    ||     || |    ||| || ||  |  |  || |            ||  |  |||| ||||| || |||||||||||||||||||| ||||| ||||| || ||  | || ||||||||||| || || ||||| ||||| || |  |||    
--------------gttggtgactattggtttctactatgtggtttggcaaataatgtggaatgtggaa-atgactttcatttgtgatctgttgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 4
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
   |||   |  | ||| | | | |  | ||  | || | | ||  | |   ||    |  | |   |  || |  | | | |        ||  |  |||| ||||| || |||||||||||||||||||| ||||| ||||| || ||  | || |||||||| || || || ||||| ||||| || |  |||    
--gttgg--tgaacattggttgctac-tatgtggttcggcaaataatgtg--gaatgtggggatgacttccatttgtgatctat-------tgggtgtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACCGATATGTACCGTGCAAACGCTATTAGAGTTCTTTGTCGTATTATCGACTCAA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
-----------------agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
                 | |||  | |  |  |||||| | ||  ||   |      |  ||| ||  | ||   ||   |  ||    ||  || |      |  | | | |  |||||||||| || ||||||||| | ||||||||||||||||||||||  ||  | || || |||||||||||  | || |||||||| ||||| |||||  
gtttcattttcttatgcaacttttcttttattttagattc-atgcgtatggtatgtgatctttattactaacttggattataaat----attctatctctttaatttttaaat--agGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
-----agcttgacatagag-----attagatacgatatgtgaaggtctgaacatt--ttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
     |  ||   ||  |      |||  ||   ||||      || ||  |  |  | |   | ||  |   || | || |  ||  || |      |  | | | |  |||||||||| || ||||||||| | |||||||| |||||||||||||  ||  | || || |||||||||||  | || |||||||| ||||| |||||  
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgttactaacttggattataaatattctatctctttaatttttaaat--agGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
agcttgacatagagattagatacgatatgtgaaggtctgaacattttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattc-cagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
         |  | |||  |  | || |       |  ||||||  |  ||       | ||||  ||      || |       |   | |    |  |||||||||| || ||||||||| |||||||||||||||| || || |  ||  | ||||| |||||||| ||  | || || || || || | ||||||  
------gtctgtaaattttactcaatttc----aatacgaacatcgtcgcacttatt-gtaggtatattttctgataagttgttggttttttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA

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|18355194|gb|BJ187253.1|BJ187253
EST:     GACGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
EST: gi|18327786|gb|BJ159790.1|BJ159790
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
EST: gi|18360932|gb|BJ192996.1|BJ192996
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
EST: gi|18359692|gb|BJ191753.1|BJ191753
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
EST: gi|18350830|gb|BJ182881.1|BJ182881
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
EST: gi|18359867|gb|BJ191928.1|BJ191928
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAAC
EST: gi|18362333|gb|BJ194403.1|BJ194403
EST:     GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAG                         GTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC
genomic: GGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGAC

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: 35 (upstream exon), 34 (downstream exon)
Score: 29

GGTGTTTTTTGCAACCACTAAATTATTCCAGTCGAGGGACATTGGTTTACGGCGCATGGTCTACATCATGATTAAAGAGATTTCTCCTTCCAGTGATGAGgtaatccgtg ... ctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG
                        acaatattaa  TA-rich tract