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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttaatatccattactcttctcttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT

Basic information

species Physcomitrella patens
transcript PP1S81_165V6.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 4
gttcttaatatccattactcttctcttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
                                        | |||     | ||       || ||| |  | |     |  ||   | |    | |      |||||| |    |||    ||||      || | || ||  |||| || || ||||| |||||||||||||||||||||||  | ||||| ||  | || ||||| ||  | ||| | ||||||||| || 
---------------------------------------gtatgatatgctgccccctcttttaactattgaaactcatcactt-gcgcgtgggctaacagaaacatttgg----acttgaacctt-----tagGTTTATTTTGAGTCAGATGAAGTGAAAGCATGCATTGTAACTTGTGGAGGCCTTTGCCCTGGTCTTAACACTGTCATCAGAGAGCTCGTCTGTGGTTTGG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
---------------gttcttaatatccattactcttct--cttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccg---cagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
               | | || | || |  ||| ||  |  |     |   || |||   | | |||    ||  | | | ||  |    ||||  ||||  ||     |   | |||      ||| |   |  || |  |||||      || |||| ||  |  |||| || ||  | ||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| |||||  | |
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaacctt--gtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
gttcttaatatccattactcttctcttgatttttaggtaatttga-atacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
                          | |     ||  ||| | | ||   || |    ||| || || |||| ||    | || |||||  ||| |  | ||   |     ||    ||||   |       || |||| ||  |  |||| || ||  | ||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| |||||  | |
------------------------gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaa----ccttgtaagtttctttcgttctttgtaacctctggttgtcttggtt-------agGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
gttcttaatatccattactcttctcttgatttttaggtaatttgaa---tacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
||   | |     || | | ||| | | ||| |  | ||||   ||   || | |  | |   |  |  |   |  ||  |  | | |   | |||||    || |  |  |||||     |||  |||||    || |||| ||  |  |||| || ||  | ||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| |||||  | |
gtatatgaaccttatgatttttcgcat-attgtacgctaataaaaaagctagaaataagggggagatgatactactaaacg--tgtatgctttacttcattcttcgtaacctcgtg-----cttgtcttgttt--agGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 4
gttcttaatatccattactcttctcttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
                                                             | ||       ||| || || |  |  ||      |  |||   |  |  |||  |  | | ||  |    || | || ||| || | || || ||    || ||||| || |||||||||||||||||||| ||||| ||||| |||||| | || ||||| |||||  || 
------------------------------------------------------------gtataaaacatggaaatgtctgtccatttg----taatctttagtaactgatgatgccttcttctaatat-tagGTTTATTTCAAGCCAGAAGAAGTACGTGCTTGCATAGTGACTTGTGGAGGATTATGCCCAGGAATTAATACAGTGATTAGGGAAATTGTATGTGGCTTGA

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 4
gttcttaatatccattactcttctcttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
                                              ||  |  |  |   | | |    | |  | ||| |||  ||     |   | | |  | ||       || |||||||  |  | ||| | || ||| |||| ||||| ||    || || || || || ||||||||||| |||||||||||||| || |||||||| ||||| || |||||  || 
---------------------------------------------gtatttgtcttgtccaatcatgcactaagaatgcttttggaatca--tggaaatataaatat------gcagtctttcc--gatctcagGTTTATTTCAAGTCAGAGGAAGTACGTGCTTGTATAGTGACATGTGGAGGATTGTGCCCCGGAATCAACACAGTGATTCGGGAGATAGTATGTGGCTTGA

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|162199151|gb|FC374597.1|FC374597
EST:     ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAG                         ATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA
genomic: ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAGgttcttaata ... ttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA
EST: gi|67569904|gb|BJ942728.1|BJ942728
EST:     ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAG                         ATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA
genomic: ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAGgttcttaata ... ttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA
EST: gi|18361584|gb|BJ193650.1|BJ193650
EST:     ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAG                         ATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA
genomic: ACACTGCTGGGGATGGTGTTCATTTCAGACGTGCAGGACCTCGTGATAAGgttcttaata ... ttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT
                   ttttgac  putative branch site (score: 3)
                                   cactctttccttgtcc  putative PPT