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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA

Basic information

species Physcomitrella patens
transcript PP1S204_102V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaat-tttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                                                                                |||| || |   |      |   | |       |  | |||  | |||   |  |||     |  |  |||   ||    | ||| |  ||  || |   ||||| ||||||||||| |||||||||||  ||||||| || || || |||||||| ||| ||||||||||||| || |||||   |||||||||||||||||
-------------------------------------------------------------------------------cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaagga----agtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                                                                         || | |   ||     |   | ||  | ||||        |  | |||  | |||   | |||| |   |  || |||   ||    |||   |   ||   |   ||||| ||||||||||| |||||||||||  ||||||| || || || |||||||| ||  ||||||||||||| || |||||   |||||||||||||||||
------------------------------------------------------------------------gttgtgtacaatacaagtgatc-tcttttgataca------gactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtg---tgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 16
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttg--cagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                                                                                   || | ||     |   |  | |   |||     |  |     | |||  |    |||   | ||  | |   |||  |   | |  ||   |||||  ||||||||||| ||||| |||||||||||| |||| || || ||||| ||||| || ||  |||||||||| || ||||||||   ||| |||||||||||||
-----------------------------------------------------------------------------------ttctgttgtgattaaataaaaacgacacaattctgatgctacttttgtctgattttcggggatacatattt-actttaggtatttattattttttgtacagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 16
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttg--cagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                                                                                    | || |            |   | ||||| || ||   | || |  || ||  |||   | |||  |    |||  |   | |  ||   |||||  ||||||||||| ||||| |||||||||||| |||| || || ||||| ||||| || ||  |||||||||| || ||||||||   ||| |||||||||||||
----------------------------------------------------------------------------------tctgttgtgattaaataaaaacgacacactt-ctgatgctacttttgtctgatt-ttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 16
-----------------gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgc-aagttttttattttattttattttattt----tatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                  | ||   || |   || |||||      |   | | |       | |  |   || ||  ||| |   |    |  ||||     |||  |  |     |   | ||  ||||| | |  || |  ||||       |||   | ||| |||   ||        ||   |  |||   ||||||||| ||||| || || || || ||||||||||||||||| ||||||||| |||||||||| || ||| |||| ||||| |||  ||||||||| |||||||
gtaaatttcactcctgcttgatgattttaaaatccgaaataacatgtcggtttatgaaaaaagaaagcatgaaattcgttactaggtccagtcctattggtaatatactcgtgatgatgattagagttctcagtagtctactaaattta------atataccattgctatgaatg-------gatatatgtttgtgatttgcagCTCAAATTCCCGATAAAGCCTGCTGATCTGAAGAAGAGGATTGAGAGCTTGATCGATCGAGAATATTTGGAGAGGGAAAAAAGCAACCCTCAGATATACA

upper sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
                                                                                 ||  |   ||     |||   |  |     |||||     ||    |||    | ||      ||   ||    |  |   |   |  ||  ||    ||||| ||||||||||| || ||||||||| ||||||| || ||||| ||||| |||||  ||||||| || ||  ||||||||  |||||| || |||||||
---------------------------------------------------------------------------------tagatagctaatgacccggttaggtggagattgctgggg-gagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

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|162226796|gb|FC403829.1|FC403829
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
EST: gi|162152351|gb|FC328538.1|FC328538
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
EST: gi|162263592|gb|FC440102.1|FC440102
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
EST: gi|162168792|gb|FC344782.1|FC344782
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
EST: gi|162226810|gb|FC403830.1|FC403830
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
EST: gi|18333234|gb|BJ165248.1|BJ165248
EST:     CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG
genomic: CACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTG

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: 15 (upstream exon), 21 (downstream exon)
Score: 1

ATTGACGCTGCCATTGTCCGGATCATGAAAACACGAAAAGTGTTAAGTCATACATTGTTAATAACAGAACTATTTCAGCAGgtaatacgtt ... aattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA
     tataattctttgttat  TA-rich tract