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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTCCAGCTATGGCACAACTGCTTTCAAATACACTTTACTACAAGCGATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagatctgtctcgtcaaatacatttacgtggtactagtatcgtctgtattacattgtttggtaggctttgatcgacttcatattaggaatatcgg...

Basic information

species Physcomitrella patens
transcript PP1S197_22V6.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_22V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os09g32800.1 (Oryza sativa), 5'ss of exon 4
AGCTGTCCAGCTATGGCACAACTGCTTTCAAATACACTTTACTACAAGCGATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgta---cgtagatctgt-ctcgtcaaatacatttacgtggtactagtatcgtctgtattacattgtttggtaggctttgatcgacttcatattaggaatatcgg------------
||||| || || |||||||||||||| || || || || ||||||||||||||||| || ||||| || || || || ||||||||  | || | ||||||||    | |||| | |  |  |    |   |     |   | |  | |  | ||| ||   |||     ||    ||  || | |   || ||   | ||               
AGCTGCCCTGCCATGGCACAACTGCTCTCCAACACTCTGTACTACAAGCGATTCTTCCCATATTATGCTTTCAATGTACTTGGTGGGCTTGATAGTGAAGgtaaggtgcagatttttatttatgttttttctccttttccaatttatgttttatgtgtt-tgttgaagcatatatatttctctaatagctaataaacacatatcttattttcacag

upper sequence: PP1S197_22V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 4
AGCTGTCCAGCTATGGCACAACTGCTTTCAAATACACTTTACTACAAGCGATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgta---cgtagatctgt-ctcgtcaaatacatttacgtggtactagtatcgtctgtattacattgtttggtaggctttgatcgacttcatattaggaatatcgg------------------
      || || |||||||||||||| || || || || ||||||||||||||||| || ||||| || || || || ||||||||  | || | ||||||||    | |||| | |  |  |    |   |     |   | |  | |  | ||| ||   |||     ||    ||  || | |   || ||   | ||                     
-----CCCTGCCATGGCACAACTGCTCTCCAACACTCTGTACTACAAGCGATTCTTCCCATATTATGCTTTCAATGTACTTGGTGGGCTTGATAGTGAAGGTAAGgtgcagatttttatttatgttttttctccttttccaatttatgttttatgtgtt-tgttgaagcatatatatttctctaatagctaataaacacatatcttattttcacagggaaag

upper sequence: PP1S197_22V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM5G817037_T02 (Zea mays), 5'ss of exon 4
AGCTGTCCAGCTATGGCACAACTGCTTTCAAATACACTTTACTACAAGCGATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagatctgtctcgtcaaatacatttacgtggtactagtatcgtctgtattacattgtttggtaggctttgatcgacttcatattaggaatatcgg
||||| || || |||||||| || || || ||||| || ||||||||||||||||| || |||||||| || || ||||| |||||  | ||||  || |||| ||   | |||  | | |  | |    |  |  |  | | | |      || |   ||||  |||  |||  |  |                     
AGCTGCCCCGCCATGGCACAGCTCCTCTCCAATACCCTGTACTACAAGCGATTCTTCCCATATTACGCCTTCAATGTGCTCGGTGGGCTTGACAGCGAGGgtaagt---tttgttgctttagtttctcccatttcttgtttgaa-cactcaaataagcatgttctgta--cttgcacag---------------------

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|208359340|gb|DC939107.1|DC939107
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAA
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAA
EST: gi|208364450|gb|DC954525.1|DC954525
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACACATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|18341261|gb|BJ173295.1|BJ173295
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|37852978|gb|BJ610986.1|BJ610986
EST:     TTCTTTCCNTATTACGCATTTAACGTGNCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: TTCTTTCCCTATTACGCATTTAACGTG-CTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208392219|gb|DC929480.1|DC929480
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208377412|gb|DC927072.1|DC927072
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162168953|gb|FC345635.1|FC345635
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208366765|gb|DC940079.1|DC940079
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAN                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTC
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTC
EST: gi|37837799|gb|BJ595807.1|BJ595807
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208368331|gb|DC955528.1|DC955528
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162168952|gb|FC345634.1|FC345634
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208379303|gb|DC927286.1|DC927286
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208368886|gb|DC947444.1|DC947444
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208371088|gb|DC955936.1|DC955936
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162186319|gb|FC361627.1|FC361627
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|37833061|gb|BJ591073.1|BJ591073
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208358782|gb|DC942948.1|DC942948
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTGGGTTCCTACGAAC
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAAC
EST: gi|67725639|gb|BJ975898.1|BJ975898
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|100446728|gb|CJ971027.1|CJ971027
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAN                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGA
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGA
EST: gi|208365808|gb|DC955439.1|DC955439
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|37840277|gb|BJ598285.1|BJ598285
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162266012|gb|FC442697.1|FC442697
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208373759|gb|DC952722.1|DC952722
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208367768|gb|DC944014.1|DC944014
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208374709|gb|DC948667.1|DC948667
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162209736|gb|FC385670.1|FC385670
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208371358|gb|DC952119.1|DC952119
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|208388708|gb|DC941521.1|DC941521
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACACATGACGCTGTTGGTNCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
EST: gi|162186318|gb|FC361626.1|FC361626
EST:     ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAG                         GTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG
genomic: ATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagat ... tggcacgcagGTAAAGGCTGCGTGTACACATATGACGCTGTTGGTTCCTACGAACGTTCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTCCAGCTATGGCACAACTGCTTTCAAATACACTTTACTACAAGCGATTCTTTCCCTATTACGCATTTAACGTGCTTGGTGGCTTGGACAATGAAGgtacgtagatctgtctcgtcaaatacatttacgtggtactagtatcgtctgtattacattgtttggtaggctttgatcgacttcatattaggaatatcgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG