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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGGGGAGTAGCTCGTGCCCGTGCATTTGCTAAAAAGTTGTCAGATGCTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaacattagcattaagaccaactccactcaatcatacaatgtgtgtgtgcaatttacgacctatcattcttctctgcgaaatgttctgatgcat...

Basic information

species Physcomitrella patens
transcript PP1S42_193V6.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S42_193V6.3 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
TGTTGGGGGAGTAGCTCGTGCCCGTGCATTTGCTAAAAAGTTGTCAGATGCTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaacattagcattaagaccaactcca----ctcaatcatacaa-tgtgtgtgtgcaatttacgacctatcattcttctctgcgaaatgttctgatgcat
|||||| || || ||  | || ||||| ||||| |||||| |||||||||| || ||||||||||| || ||| |||| ||||| ||||| ||  | |||| || |   | |   |  |   |    ||  |       |  ||  ||| ||  ||| |  |    |  |  |||||   |  |     |||| ||    |    
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaa-tatcaacttcatagcttaaatattagttt----

upper sequence: PP1S42_193V6.3 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 5
TGTTGGGGGAGTAGCTCGTGCCCGTGCATTTGCTAAAAAGTTGTCAGATGCTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaacattagcattaagaccaactccactcaatcatacaatgtgtgtgtgcaatttacgacctatcattcttctctgcgaaatgttctgatgcat--
|||||| ||||| ||| | || ||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||| |  | || ||||| || ||| |||||||||  ||  ||| | |  ||  | |||     |  |  |||          |   | ||        ||   |     || |    ||   |  | |||  
TGTTGGTGGAGTTGCTAGAGCGCGTGCTTTTGCCAAAAAATTGTCAGATGCACCTCTAGCCATTGTGGATAAAAGGCGCCATGGGCACAATGTTGCAGAGgtaacaca-tatttgaac-aaatctaacaatggtttacaatattggtaaaaagcctagttgtttgttgatttcttcatccttcattttggcttattacatct
















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|162252374|gb|FC427287.1|FC427287
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|162173033|gb|FC349165.1|FC349165
EST:     AGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: AGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|67693971|gb|BJ954204.1|BJ954204
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|162176833|gb|FC353341.1|FC353341
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|208350468|gb|DC926201.1|DC926201
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|67693854|gb|BJ954087.1|BJ954087
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|162176832|gb|FC353340.1|FC353340
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|208397845|gb|DC916166.1|DC916166
EST:     CTCCGCTAGCTATTGTGGACAANCGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|208351272|gb|DC921551.1|DC921551
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|162261957|gb|FC436816.1|FC436816
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|162252375|gb|FC427288.1|FC427288
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|18341516|gb|BJ173551.1|BJ173551
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
EST: gi|67694322|gb|BJ954555.1|BJ954555
EST:     CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAG                         GTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT
genomic: CTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaac ... ggcgtggtagGTGATGAATCTCATCGGAGATGTCAAGGGAAAGGTGGCAGTAATGCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGGGGAGTAGCTCGTGCCCGTGCATTTGCTAAAAAGTTGTCAGATGCTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaacattagcattaagaccaactccactcaatcatacaatgtgtgtgtgcaatttacgacctatcattcttctctgcgaaatgttctgatgcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA