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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT

Basic information

species Physcomitrella patens
transcript PP1S165_107V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 3
attatgataa-caacaacaataaaactaattgtaacaatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctc-tgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
|||  | |   |     |  |     |   | ||  |  ||     |    |  |    |   |||||   |    | | | | | | ||||    || ||||| ||||| ||||||||||| ||||| || |||||||| || ||||| || || ||||| |||||||| |||||||  || ||  |  | ||||| ||||
attcagttgggcttgttcggtgttcgtcgatttagtagccaggacttat--ttctaatctcctgttatcttttttctaaattccgtcctgcttaccttccagGCATTGGATTACTGTCATTCTCAAGGAATTATGCACCGCGATGTCAAGCCTCACAATGTTATGATTGACCATGAACTCCGCAAGCTTCGCTTAATTGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 3
attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggta-ttttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
|  |   | |     |   |     |   | |  |   |    | |     |   | ||      || |  |    | |  | |   |   |   || |||||| | || ||||||||||| ||||| || ||||| ||||| ||||| || |||||||| ||||| |||||||| |  |||||| |  | || ||||| |
accaatgtgatttagatcttgtg-ttctctctggcggcctgcctttatttcaacctacaacctactagttgttatgtaataattatttcttttaattccagGCCCTTGATTACTGTCATTCTCAAGGCATCATGCATCGAGATGTCAAGCCCCATAATGTAATGATAGATCATGAGCTTCGAAAACTTCGGTTGATAGACT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 3
-----attatgataacaacaacaataaaactaattgtaacaatcatag-tatgaggtattttcattgggttattcatcgattgagtactggcttgctctgttt-cagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
      || || | |   || ||  |||| || ||   |  | || |   ||| | |  |  | ||    |  |  |   |||| | ||   | | | ||  |  ||||||| || ||||||||||| ||||| ||||||||  |||| ||||| || |||||||| ||||| |||||||||   || ||| |  | || |||||||
ataggcttttgcttatg-catcatgaaaattacttcacattagcacaaacatgtgttgatgacctt----ttcttgttacttgaatgct--ttagttttgaatgtagGCCTTAGATTACTGTCATTCTCAAGGCATAATGCATAGAGATGTCAAGCCTCATAATGTTATGATAGATCATGAATTACGGAAACTTCGCTTGATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 3
attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctctg------tttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
         | |      || ||| || || |  |||||  |  ||   |||||     ||| |   ||| |     ||  ||   ||  |  |      |  |||||  |||| || || ||||| ||||| || ||||| || || || |||||||||||||| |||||||||||||| ||||| ||  |  |  | |||||||
---ggatctatagtttgcattaaattatttttt-caatccaaccatttcgtattgcttgtggcta--tcaacttggaagcgctaagttatttggaatttctgccagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 3
attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctctg------tttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
  |    ||  |    ||||| |  | ||| || |||||  |  ||    ||||     ||| |   ||| |     ||  ||   ||  |  |      |  |||||  |||| || || ||||| ||||| || ||||| || || || |||||||||||||| |||||||||||||| ||||| ||  |  |  | |||||||
--tgatctataatttgcaataga--ttattttatcaatccaaccatttcctattgcttgtggcta--tcaacttggaagcgctaagttaattggaagttctgccagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
attatg-ataacaacaacaataaaactaattgtaacaatcatagtatgag-gtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
 | ||      |   | | | |||| || |  |||  ||   || |   | ||||| | |     ||     |    ||| | ||    |  |   || ||||||||||| ||||| ||||| ||||| || |||||  | || ||||| || |||||||| ||||| ||||||||    |||||| |  | || |||||||
-tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacct-ttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 3
-attatgataacaacaacaataaaactaattgtaa-caatcatagtatgaggtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
  ||    | ||   |    | || | | | |    || | |||    |    | |||  ||  | |  |  | | |    | ||   |  |  |  | ||||| ||||| | ||| ||||| |  || || |||||| |||| || |||||||||||||| ||||||||||| || ||||||||| |  | ||||| || |
tgtttaccttacttgacttttgaatccactagccttcagttataaagggtacgaatttgtttctgatgctgtttgtt--gtttctttttaacatttatgcagGCGTTGGATTTCTGCCATTCACGTGGAATCATGCACAGAGATGTGAAACCACATAATGTCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 3
attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggtattttc-attgggttattcatcgattgagtactggcttgctctg-tttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
 | ||  |   ||     |  |||||| | ||  |   | |    | ||   |  ||   | |  || |  |  |     | |||  ||  |    | |||||| || || ||||| ||||| ||||| ||||||||  |||| |||||||| || ||||| |||||||||||||| |  || ||| |  | || |||||||
-taattctttaaattggcaacaaactattggttcctgccttgaactcagcagtcctctgatagactactttttaaacttat-ctgatttatttgaatatcagGCATTAGATTACTGCCATTCACAAGGTATAATGCATAGAGATGTCAAACCTCACAATGTTATGATTGATCATGAGCTTCGCAAACTTCGCTTGATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 3
-attatgataacaacaacaataaaactaattgtaacaatcatagtatgaggt--attttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
 |||   |||    ||   ||   || || | |     |     | | ||||  | |||||||  ||||    | | | || |  |    |       | ||||| || || ||||| || || || || || ||||| ||||| || || ||||||||||| |||||||||||||| ||||| ||| |  |  | |||||||
cattggcatattg-catatattttacgaagtattcatgttggtttgttaggtgaactttcatttagttaac--ttggtagaatctttttctttatatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCACATAATGTCATGATTGATCATGAGCAGCGTAAACTTCGTCTTATAGATT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 3
-attatgataacaacaacaataaaactaattgtaacaa-tcatagtatgaggtat-tttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
 || |    |||   |     |  |  |     ||||  ||| | | |      |  ||| ||   |  ||  |  ||| ||||  | |||||     | ||||| || || ||||||||||| ||||| ||||||||| |||| ||||| || || ||||| ||||| || |||||   ||||||| | ||| | || ||||
tatgaaacaaactggaggctcagcatcacagagaacatctcaaattgttgcaagtgcttcttttcatgcttgcttaattcagtaa-gtcttgcgta--tgcagGCATTAGATTACTGTCATTCACAAGGAATAATGCACAGAGATGTCAAGCCTCACAATGTTATGATAGACCATGAGTTGCGAAAACTTAGACTGATTGATT

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|22133106|gb|BQ827548.1|BQ827548
EST:     CGACGCTGACGGACTATGACATACGGTACTATATTCACGAGCTCTTGAAG                         GCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCA
genomic: CGACGCTGACGGACTATGACATACGGTACTATATTCACGAGCTCTTGAAGgtagtgtctg ... tctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
                                            ctctgtttc  CT-rich tract
     tattttcatt  TA-rich tract