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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------------------catgtttccaaccctctcttcgttctc--ggtatcaaatttcgtaaa-------tcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
                                                                          ||||    |         | ||| |    | ||||  |||   | |           |  |  || | | |     | || |||        | |  ||| ||| ||||| |||||||| || ||||| ||||||||||| |||||||||||||| || ||||| |||||||  || ||||| ||||||||||| ||| | |||||  
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggct-actctg-tttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g51380.1 (Oryza sativa), 3'ss of exon 8
---------catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
         |||          || ||||     ||  |||     |   |||   | |      |   | |  |      || |||||| ||||    |  ||   |||| ||||||||||| || |||||||| ||||| ||  ||||||| ||||| || || ||||| |  || |||||||| |||||||||||  | ||||| |
gtatatctgcattacctttgttctttcttttccttcactatgctgctc--taaggaatttgcaagatctataacttactccttgattttgtattt---tttgttcatagGCAAATGATCCAACTATCGAGCGTATTATCACCCCAAGAATTGCTCTCACCACAGCAGAATACTTGGCATATGAGTGCGGGAAGCATGTTCTTGTCATCC

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttga-atttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
  | |   |   ||   | |     |  |    | || |  || ||  |   |     |   ||  |      || |||| | |  |  |     || |||||||||||||| || ||||| ||||| ||||| ||||| ||||| || || || || |||||||  || ||||| ||||||||||||||  | |||||  
-ctatcctctggccctgcataacgatgagccaaatatattctacatgtgacataatcagtgtatagcacagcatatttttaacaccttgatcctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
----catgtttccaaccct-ctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
    ||   ||  ||     || || | | ||       | || | | ||  ||        | || || |  | ||   | | ||||| | |  |    ||||||| |||||||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||  |||||||| ||||| ||||| ||  | || ||||
aaagcaaaatttaaatgaggctttttgatttc----ctgacttgcatgaaggagc-taatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatca-gtgctggaac-gaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
  |||     | | |    |  || ||    |   ||||| | |      ||  ||||| || ||||     | |   |||||    | |  |   ||  |||| |||||||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||  || ||||| ||||| ||||||||  | || ||||
--tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
----catgtttccaaccct-ctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
    ||   ||  ||     || || | | ||       | || | | ||  ||        | || || |  | ||   | | ||||| | |  |    ||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||||||||||  |||||||| ||||| ||||||||  | || ||||
aaagcaaaatttaaatgaggctttttgatttc----ctgacttgcatgaagtagc-taatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 8
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatca-gtgctggaac-gaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC-
   ||     | | |       ||  |    |   ||||| | |      ||  ||| | || ||||       |   | |||    | |  |   || ||||| |||||||| || ||||||||||||||||||||||| ||||| || ||||||||||||||||  || ||||| ||||| ||||||||  | || |||| 
---gtggatgatcattgtgctatttgcaaattttgatttcatgacctgtatgaaggagctgatcattaaaatcctgtctcttgttgctgtgatttattacaggCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATACT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttg-cagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
                   |  | | |    | |||  | |  |  | | |  | | |||   |  |  |   |  | || |  |   || |  ||   ||  || |   |    ||||| ||||||||||| |||||| | || ||||||||||||||||| || || || ||||||||||  |||||||| ||||| ||||||||| | || ||| 
gtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattat-atcagtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 8
catgtttccaacc-ctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgattt--gcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
  |   |   ||  || |    | |  |  |||||       |     |||  |   | |    ||   | |    |  || ||  |    | |||    ||||| ||||| ||||| |||||| | |||||||||||||||||||| ||||| || |||||||||   |||||||| |||||||| || ||  | || ||| 
-gtaaatttgacttctatagctgattgccatatcatggagttttttcaagtatttagatgtttcttagctttaaacagatttaaccttcctttattccaacagGCCAATGACCCAACCATTGAGAGAATCATCACTCCTCGAATTGCCCTCACAACAGCTGAATATCTGGCTTATGAATGTGGGAAACACGTCCTTGTTATAT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
        |||  ||| |     || |  ||   |  |    ||   | |  | |  | ||  |||  | |     |||   |||     |      ||||| || || || || ||||||||||||||||||||||| || ||||| || |||||||| || |  || ||||| ||||| ||||||||  | ||||| |
-------gcaagtctcgc---aatcacactacagacatcttgaagcaaattttagttccaatgtttt-tctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 8
---------------catgtttccaaccctctcttcgtt-ctcggtatcaaatttcgtaaatcagt--gctggaacga-acatttcgtgttttaat-tttgaatttatactgattt-----gcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
                   | ||  | |||   |  |||  |  | || |  | ||  |  ||| |  | ||||| |     |||  | ||||||| |||| | | ||   | | |      ||||| |||||||| || || || || || ||||||||||||||||| ||||| ||||| |||||||  |||||||||||||||||||||||  | || ||| 
gtatcaattaataatttaatctcttatcctaattatgttgtttaggatgatctctctcatttcatttaggtggaagggtgttttttttcttttaatatttgtaatgatgtggctcttttgcacagGCCAATGATCCCACCATAGAACGCATTATCACTCCTCGAATTGCTCTCACAACTGCAGAATATTTGGCTTATGAGTGTGGGAAGCATGTTCTAGTTATAT

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
----------------catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaac--gaacatttcgtgtt--ttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
                 || |         | |  | |||   ||| | |||||    |  | |   | ||     ||| | || |  ||   || |||   || |   |   |   ||||| || || || || ||||| || |||||||||||||||||||| ||||| |||||||||||||  || ||||| ||||| || |||||  | |||||||
gtatttatattaaattaatatagtggtatttattattgtttgtggtgt-aaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

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|162269043|gb|FC445535.1|FC445535
EST:     ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG                         GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
EST: gi|162221566|gb|FC397583.1|FC397583
EST:     ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG                         GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAA
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAA
EST: gi|162278567|gb|FC454029.1|FC454029
EST:     TTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTNCA-TTTG                         GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCAC
genomic: TTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCT-CAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCAC
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG                         GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG                         GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
                                          tactgat  putative branch site (score: 2)
                       tgttttaattttgaat  TA-rich tract