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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 11
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactc-ttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || |||||||| || ||||||||||| |||||  | |||||||| |||||||| |||||||| || || |||||| |||| |||||||| || ||||||   |     ||  |  |     |  ||   |||   |       | || |   | |   || |  |  | |  |                                                                                                             
ATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGGGGCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacag------------------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagct--tttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || |||||||| || ||||||||||| |||||  | |||||||| |||||||| |||||||| || || |||||| |||| |||||||| || ||||||   |    |||  || | | |   | ||| | |||     ||    | |   |  ||   ||| |  ||| |  || |                                                                                                          
ATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGGGGCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaatatacaagttcat-cagctatcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacag----------------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA09G38110.1 (Glycine max), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattt--tagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || |||||||| || || || |||||||||||| | |||||||| || ||||| |||||||| || || |||||| |||| ||||| || || ||| ||    ||   |  ||   |  | |   |  || |  ||  || ||  | |||    |  |   | ||| || |||| |   |  |                                                                                                    
ATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGGGGCGAAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCTAATGATGgtgatgaaatattattgaatcttatcagctatcatgcataat--gcactctcaatt---ctgactgattgtttttcttgaacttctgtacag-------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaatttta-gcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgct-tacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
 |||| || |||||||| || || || |||||||||||| | |||||||| || ||||| |||||||| || || |||||| |||| ||||| || || ||| ||   |        | ||||    |  | |  |    |  || ||  | |||  ||      ||| || | ||  ||  || ||||                                                                                                    
-TGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGGGGCGAAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCTAATGATGGtgatgaaatattattgaatcttatc-agctatcatgcattatgcactctcaatt--ctgactgattatttttcttgaacttctgtacaga--------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactcttgctgaatttttgtaagattagc--gctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || |||||||| || ||||||||||| || ||||||||||| ||  | || || || ||||| || ||||| ||  | ||||||||||| ||||||||||||    |   |   ||  || |||    | | || |      |   |||||       ||     | ||| |      |   ||    |||                                                                                            
ATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAGGAAGAAAGGGTTCCATTACCCAAATCCCTATCCTGACTATGCCCAATGACGgtaatttt----ttttatcgtttttggattccattcatatcaaatgttttttgattaaacaaagctcataatatttcttgttatt---aaaactcag--------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagc---ctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgctt-acaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
|||||||| |||||||| || ||||||||||||||||| ||||| || ||  | ||||| || || || || || |||||  | ||||||||||| ||||||||  | | |   || || |   | |  |  || | |    |       |   | |   || |   |   |  | ||||||   || |  ||                                                                                                  
ATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAGGAAGAAAAGGTTCCATCACCCAAATTCCAATCCTCACTATGCCCAATGACGgtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcag--------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactcttgctgaatttttg-taagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || ||||| || || |||||||||||||||||||||||||| || || || || || ||||| || ||||||||||||||||||||||| || |||||| | |  |   | | | |  |||  |  || | ||| |  | |     | | ||  | |  | |  |     |||    | |||                                                                                                    
ATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAGGACGGAAGGGTTCCATTACACAAATCCCAATTTTAACTATGCCCAATGATGgtaatgtcaagcatcatc-catattgatctagtggtgagaatttctcattatagtggcactacactca-ctgaacctgatt-ttcacag---------------------------------------------------------------------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 10
ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcag
||||| || |||||||| || |||||||| |||||||||||||| || || || ||||| || || || || || || |||||||| ||||| || || |||||| ||||| |       || | | || | ||     |   | ||||  || || | ||    ||||        |   | |  ||           || | |||||| | ||  |  |                                                                  
ATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAGGGCGAAAAGGCTCCATCACACAAATTCCTATTTTAACCATGCCTAATGATGgtaatgttagcat-------tttcaggatgtctggctattcttccctgcacatcagttcttgtaatagtgaacagacattacctgaaa-----------ccaattattttttgtccaccag------------------------------------------------------------------

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|208395424|gb|DC924478.1|DC924478
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162269043|gb|FC445535.1|FC445535
EST:     CCGTANAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCC
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCC
EST: gi|37837091|gb|BJ595099.1|BJ595099
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162153494|gb|FC329380.1|FC329380
EST:     AACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: AACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162278566|gb|FC454028.1|FC454028
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162230898|gb|FC406737.1|FC406737
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|67698241|gb|BJ958474.1|BJ958474
EST:     GTAAAGGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAG
genomic: GTAAA-GGATCTATTACTCAGATCCCAATTTTAACTATGCCCAAC-GACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAG
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162153495|gb|FC329381.1|FC329381
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA

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), 28 (downstream exon)
Score: 6

ATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGGGCCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG




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