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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatattagaacgtt...

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 7
---GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGG-AGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatattagaacgtt-
    |||||||||||||||||||| || || || |||||||| || |||||||| || ||||| |||||  || | ||||||||||  ||| ||     || ||   || |  |    || ||  | |||   ||| || |   |  |    ||   |    ||||    ||   | ||       | |   || | | || |  
CCTCTTTTCTGCTGCTGGTCTTCCTCATAATGAAATTGCTGCCCAAATTTGTCGTCAGGCTGGCCTTGTGAAAAGCTTGGAGAAAGGCAAGCATGCAGAGgtagccaagcatttctctcacataaagata---atctgactatttgatgacccag--tgagatttgggctcacatatatagcttaataactttagttgtacatgg

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 7
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattgaaatatgtatcagat-tgacttctacttcatgcttttgtttgtctgcaagcac-atgctagggttatcatattagaacgtt
|||||| ||||||||||| || ||||| || |||||||| |||||||| || || |||||||| ||  | || || |||||     | ||| |||||||||| |      | |  |      |||||  |||| |  | |||       |||     ||||    |    | ||  |   | | |      ||||   | | 
GTTTTCCGCTGCTGGTCTCCCACACAATGAAATTGCTGCTCAGATTTGCCGTCAGGCTGGTCTGGTAAAGCGTTTAGAGAAGAGTGACAATATCTTGGAGgt-atttttgtctaaactacataatattcatcatacctaactggagtaccatttccatgttgcattctgggtactgtagcaagctataggcattacttctt-

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 7
---GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattga---aatatgtatcagattgacttctacttcatgcttt---tgtttgtctgcaagcacatgctagggttatcatattagaacgtt
   ||||||||||||||| || || ||||| || |||||||| ||||||||||| || |||||||||||  |    |||||||||| |||| ||     ||  |  |     || |   |  | |    |    ||   |  || | ||  | | || |        | | | |    |||||  |    |  | || ||         
ACTGTTTTCTGCTGCTGGGCTCCCTCACAATGAAATTGCTGCTCAGATTTGTCGTCAGGCTGGTCTTGTGAAGACATTGGAGAAAGGAAAGCATGCTGAGgtagctaatgtgttctaacttctaactgcaaccctactggcatgccctcccccttatccaaaaaacatatttttcagtgcacaaacagttgaaaacacat---------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 7
---GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatg---ctagggttatcatattagaacgtt
    |||||||||||||| || || ||||| || |||||||| ||||| ||||| || ||||| |||||  |    |||||||||| |||| ||      |||||    |   | | |  | || ||    || |   |   || |      |    ||| |  |  | ||| ||  ||     |    |    | ||| ||    
CCTATTTTCTGCTGCTGGACTCCCTCACAATGAAATTGCTGCTCAGATCTGTCGTCAGGCTGGCCTTGTGAAGACATTGGAGAAAGGAAAGCATGC---AGAGgtagctaatgtgtcctaactgcaaccc-taccccctcccctacctacaaacatatttttcagagtacaaacagttgaacacacatctgcactcttaaaaaa--

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 8
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgagg-accttatgcat-attgaaatatgtat-cagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatatt-agaacgtt
 |||||||| || |||||||||||||| || |||||||| |||||||| || || |||||| | ||  | || || |||||   | | |||||  | |||||        |||| ||| | ||     ||| | ||| | ||  |    ||  | |  || |    | |  | | | |     | |   ||||   |  ||   
CTTTTCTGCCGCAGGTCTTCCCCACAATGAAATTGCTGCTCAGATTTGCCGTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAGgtatcacgatttatacattactggtccgtgtctacagttggaaattggtttgttacaattat--aacagtgatcccttagacagttagacatacccattaca--

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 7
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatattaga-acgtt
 || ||||||||||||||||| || || || || ||||| ||||||||||| || |||||||| ||| | || ||||| ||        ||||  | ||||| |     |    | | |  |||||| | ||  |||    | |||   | ||| || ||||  |   | |   | |||    | |  |  | ||   || 
TTTCTCTGCTGCTGGTCTTCCACATAATGAAATAGCTGCTCAGATTTGTCGTCAGGCTGGTCTAGTCAAGCGTTTGGAAAAGACTGTTGATCTACTTGAGgtaatcctttgtaacttgtacaaatatatctcttatttctctataccaaa-gctcttatttgagttgtaactgtttctacaagtgtgttgatggatgtgtg

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 7
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCT--CTTGGAGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatattagaac-gtt-
    |||||||||||||| || || || ||||||||||| || |||||||| || ||||| |||||  | |||||||| ||     ||||  |   |  |  |  |   | ||   |  |||   |     |  | | | |||| |  ||      | |    || |    ||   |    |     |||  ||  ||| | | 
---CTCTGCTGCTGGTCTACCTCATAATGAGATTGCTGCTCAAATTTGTCGTCAGGCTGGACTTGTGAAGCGGTTGGAAAAGACTGAGAACTTAATTCAGGAGgtaaatcatttgccccattaccaccaccactaaagt-acttttgttttccaagtatcaaagtgtaagtgcctgtttctgcacattcactttctaactgatg

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 7
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgagg---accttatgcatattgaaatatg-tatcagattgacttctacttcat--gcttttgtttgtctg--caagcacatgctagggttatcatattagaacgtt
 |||||||||||||||||||| || || || || ||||| ||||| ||||| || |||||||||||  |  ||||||||||       | |||| | |||||  ||   ||    |||| |  ||||| ||  ||   ||  | ||  | | ||   | | ||| ||    |   ||  |      ||    ||  | |||       
TTTTTCTGCTGCTGGTCTTCCTCATAATGAAATAGCTGCTCAGATATGTCGGCAGGCTGGTCTTGTAAAGAGGTTGGAGAAGTCTGGAAGTCTCCTTGAGgtatggtagactcgctgcaca--gaaatttggcatttaataaaattgaattgcaaaagatgttgattagtagaataactagggcaaagaaccattgttttat------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 7
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtga-ggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcat--attagaacgtt
 |||||||||||||||||||| || || || || ||||| || || ||||| || |||||||||||  | |||||||| |||      |||||| | |||||    |   ||    || ||    | || |    ||||  ||   |    |     |  |    ||           | |  || | ||  || ||||    
TTTTTCTGCTGCTGGTCTTCCTCATAATGAAATAGCTGCACAAATCTGTCGTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAGgtactagtttttgcatattttactttctggaattcattgcatttggcaatgtaaaagtaataagatgtctctttggaattgaattgttattgataagaag---

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:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|162221566|gb|FC397583.1|FC397583
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|100392297|gb|BY953293.1|BY953293
EST:     GACNAGCTGGTCTTGTCCAACGGGTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACNATTTCTGTNAT-GTTTTTGCAGCTATGGGAGC
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGT-ATTGTTTTTGCAGCTATGGGAGT
EST: gi|100441292|gb|BY962581.1|BY962581
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGA-TCTCTTGGAG                         GATGA-CACGGCGAAGACNATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|100360601|gb|BY984200.1|BY984200
EST:     GACNAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAA-GAATCTCTTGGAG                         GATGAACACGG
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGG
EST: gi|67574817|gb|BJ947641.1|BJ947641
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|162278567|gb|FC454029.1|FC454029
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTT
EST: gi|208357262|gb|DC910659.1|DC910659
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAA-GACAATTTCTGTATTGTTTTTGCAGCTATGGGAGT
EST: gi|100432786|gb|BY978739.1|BY978739
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAAGACNATTTCTGTATTGTTTTTGCAGCT
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCT
EST: gi|100425066|gb|BY976955.1|BY976955
EST:     GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAG                         GATGAACACGGCGAA
genomic: GACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggacct ... ccttcgacagGATGAACACGGCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCTGCTGCTGGTCTTCCCCACAACGAGATTGCTGCGCAGATTTGTCGACAAGCTGGTCTTGTCCAACGGTTGGAGAAAGAAAAGAATCTCTTGGAGgtgaggaccttatgcatattgaaatatgtatcagattgacttctacttcatgcttttgtttgtctgcaagcacatgctagggttatcatattagaacgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG