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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGACCCCGACTTCATCGCTGCTAACCAGGAGGCTCGTGCGAACAATCTCATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatccatcactgagaagcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaatttatgaatatttctgaatccagctatttttggttgcag

Basic information

species Physcomitrella patens
transcript PP1S55_204V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
ACGACCCCGACTTCATCGCTGCTAACCAGGAGGCTCGTGCGAACAATCTCATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatccatcactgagaagcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaatttatgaatatttctgaatccagctatttttggttgcag
| ||||||||||||||||| || |||||||   | || ||||||||| ||||||||||  ||||||||||||| ||||||| ||| ||| |||||||  ||||  |   |||   ||  |      | | | ||||   |||        |  |  || |   |||||   |    | | |||   || | |  ||  |  |  |    | |  ||||
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaa-----ttgagcccatt-ttact--------tcataacaaaaaggaatagtattc--tgaattagttatgtctacgaggcatg--aacactaggggcag

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 4
ACGACCCCGACTTCATCGCTGCTAACCAGGAGGCTCGTGCGAACAATCTCATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatccatcactgagaa-gcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaat-ttatgaatatttctgaatccagctatttttggttgcag
| || || ||||||||||| ||||||||||   ||||||| |||||| ||||||||||  ||||||| || ||  |||||| ||| ||| | || ||  |||| ||   |||   ||  ||  |   |    ||| |   |   |  ||||        |||   || ||       || |  ||||||| ||  |  || ||                 
ATGATCCGGACTTCATCGCCGCTAACCAGGGCTCTCGTGCCAACAATGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggacatggatgctaacacacattggtgcaattaaa---gaagtgccctcagtgcagcctaaaacaaagaaatactgctatgaat-ttagtacatacac----------------
















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|162277484|gb|FC453427.1|FC453427
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGA
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGA
EST: gi|162185828|gb|FC362384.1|FC362384
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162162654|gb|FC338956.1|FC338956
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|40781590|gb|AJ583520.1|AJ583520
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162247857|gb|FC420616.1|FC420616
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162249068|gb|FC421190.1|FC421190
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCANACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162155272|gb|FC331729.1|FC331729
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162191433|gb|FC368190.1|FC368190
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162186353|gb|FC361661.1|FC361661
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162194084|gb|FC370259.1|FC370259
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162184403|gb|FC359149.1|FC359149
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162175808|gb|FC352110.1|FC352110
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162184271|gb|FC359693.1|FC359693
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162220955|gb|FC396140.1|FC396140
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162151547|gb|FC327260.1|FC327260
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162268155|gb|FC443833.1|FC443833
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|100432324|gb|BY960427.1|BY960427
EST:     TNCA-GGGTTC-AAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAG-CGCAAACCA-GGTTGACAAG
genomic: T-CAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAG
EST: gi|162156175|gb|FC332550.1|FC332550
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162172410|gb|FC349079.1|FC349079
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162167690|gb|FC344004.1|FC344004
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162173468|gb|FC349847.1|FC349847
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162197484|gb|FC372862.1|FC372862
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162256553|gb|FC432863.1|FC432863
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCANACCAAGGTTGACAAGGTAGTGGTACTGTGGAC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGAC
EST: gi|162206576|gb|FC382945.1|FC382945
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCANACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162194175|gb|FC369687.1|FC369687
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162246259|gb|FC421966.1|FC421966
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162222899|gb|FC399361.1|FC399361
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
EST: gi|162218352|gb|FC394526.1|FC394526
EST:     ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACG                         GAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC
genomic: ATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatcc ... ttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGACCCCGACTTCATCGCTGCTAACCAGGAGGCTCGTGCGAACAATCTCATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatccatcactgagaagcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaatttatgaatatttctgaatccagctatttttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA