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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtttaaatgataatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG

Basic information

species Physcomitrella patens
transcript PP1S101_185V6.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
gtaat-actcctcagtatcttattac-ggtattgttaattggactggaattacacgtattacctgtgtttaa-atgataatgtaaagtttcattcgaaattggatt-----tggagtttcgaa-----tttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
||| | |   ||| | |||  |  |  || |    |  |          |  || ||||  | | ||   |  ||  |    |   | | ||  |  || || |||     |  | ||| |||     | |  ||   || ||       | | ||  |     |  |||   || |||||| ||  | || || |||||||||||||| |||||||||||||| || |||||||| ||||| || ||||| || ||||| ||  | || ||||| || ||
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtat-gcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG

upper sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G08970.1 (Glycine max), 3'ss of exon 3
gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtt-taaatgataatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatc-ctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
                                                             | || | | |||  || || |   || |||  |  ||||  |||  | ||   | ||   |    ||  || | | || || || |||||| ||     | ||||||||| || || || || || |||||||||||  |||| ||||| ||||||||||| || || || || || ||||||||||||||||| || |||||||| ||
-------------------------------------------------------------tatgatatcaatcttattgcac--ttacatatgtcattgttttttaaatt--aagttagatcccaaaagctttggatattcacttgagtttctt-----tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGG

upper sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtttaaatga-taatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
                                                         || |    |   | ||| |  | ||  | | | |     | ||  ||||    || |   |     |  | |  |    || |  ||  | |||||       |  ||||||| ||| |||| || || |||||||||||  |||| ||||| |||||||| || || |||||||| |||||||| ||||||||||| || || || |||||
---------------------------------------------------------taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggat----aagaaggtttaacattta--cttcaatttgtg------tcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG

upper sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ21803 (Selaginella moellendorffii), 3'ss of exon 4
gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtttaaatgataatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
                                                                                                                         | | ||  ||||| |  | || | | |   | ||   || | |||||| || || |||||||||||||||||||| || || |||||||| || || || || ||||| || || || || |||||||||||||| || || || ||
-------------------------------------------------------------------------------------------------------------------------gtataacactgttttcta-ccgcaactaactcgtttcttgtttgcagATAACCTCGCGGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

upper sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ34189 (Selaginella moellendorffii), 3'ss of exon 4
gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtttaaatgataatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
                                                                                                                         | | ||  ||||| |  | || | | |   | ||   || | |||||| || || || ||||||||||||||||| || || |||||||| || || || || ||||| || || || || |||||||||||||| || || || ||
-------------------------------------------------------------------------------------------------------------------------gtacaacactgttttcta-ccgcaactaactcgtttcttgtttgcagATAACCTCGCCGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

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|37833326|gb|BJ591338.1|BJ591338
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|37829213|gb|BJ587225.1|BJ587225
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|37839981|gb|BJ597989.1|BJ597989
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|162175217|gb|FC351415.1|FC351415
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|208375549|gb|DC945108.1|DC945108
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|37833498|gb|BJ591510.1|BJ591510
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTNTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|208382616|gb|DC919798.1|DC919798
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|37832046|gb|BJ590058.1|BJ590058
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|208360731|gb|DC946455.1|DC946455
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|162162823|gb|FC338085.1|FC338085
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
EST: gi|37852866|gb|BJ610874.1|BJ610874
EST:     CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAG                         ACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA
genomic: CCTTTCGCAGACTTTTAAAGCAGATATTCTACTGTGCGAGTCTGGAGGAGgtaatactcc ... ttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG
                    tgttaat  putative branch site (score: 3)
                                             ttttctgc  putative PPT
                   ttgttaat  TA-rich tract