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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttttcagcgttgaaactatagtaaacatcacttgcagcagtccgaaagagggttagaattgaagctgttccctcaca...

Basic information

species Physcomitrella patens
transcript PP1S56_243V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g49030.1 (Oryza sativa), 5'ss of exon 3
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtat-gtgtggttgtctgaaaactttttcagcgttgaaactatagtaaacatcacttgcagcagt-ccgaaagagggtta-gaattgaagctgttccctcaca
||||||||||||||||||| ||||||||||||||    | || ||  | || || ||||| ||||||  |     ||  || |       ||   |  ||         |    |||| ||||        ||  | ||          ||   || |    | |  
GTACTTCCTGAGGAAGCTGAAGAAGGTGAAGAAGAGCAATGGACAGATGCTCGCCATCAACGAGgtaccgctcaatttgctcactttcaatttgac--tgccttgtccatgcgtatcaattgccatgacgtcgttacagatccgcaggctgccactttgatattag-

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g47660.1 (Oryza sativa), 5'ss of exon 3
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttttcagcgttgaaactatagtaaacatcacttgcagc--agtccgaaagagggttagaattgaagctgttccctcaca----
||||||||||||||||||| ||||||||||||||    |||||||  | || || ||||| ||||||   |   ||       |   | ||  ||  |||        | |    || ||| | |  ||| | | | |    |   | |||   ||  | || | |    
GTACTTCCTGAGGAAGCTGAAGAAGGTGAAGAAGAGCAACGGCCAGATGCTCGCCATCAACGAGgtactagaaattcaaacgtattgtatttcgccctgattgctccctga----catttgtaacctagttctagatattaatcatactga--ttgaccgctaataagtg

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G022619_T01 (Zea mays), 5'ss of exon 3
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttttcagcgttgaaactatagtaaac-atcacttgcagcagtccgaaagagggttagaattgaagctgttccctc-aca----
|||||||||||| |||||| ||||||||||||||    | |||||  | || || ||||| ||||||       |  |      ||  |   | |||  |   |          || | ||   |  |  |||| ||   |||| | ||      |||| |  | |    
GTACTTCCTGAGAAAGCTGAAGAAGGTGAAGAAGAGCAATGGCCAGATGCTCGCCATCAACGAGgtacaaccaatccttc----accctcgtaccgtgaacgttgctccgctttatgaattagtgtcggtcgaatgat--ttagcaatgccagcattccatagataggtg

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ38689 (Selaginella moellendorffii), 5'ss of exon 3
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttttcagcgttgaaactatagtaaacatcacttgcagcagtccgaaagagggttagaattgaagctgttccctcaca
|||||||||  | |||||  |||||||||||||| ||||||||||  |||| |||||||| ||||||    |  || | |      | ||||     |  | |  ||  ||     |  |   | | | ||  | |  |                         
GTACTTCCTTCGCAAGCTCAAGAAGGTGAAGAAGTCTCACGGCCAGATCCTCGCTATCAACGAGgtaaagttctttcttt-----ttctttcttttctcgagcctta-caagtgagaactttggaacttcgtgacacag-------------------------

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ31458 (Selaginella moellendorffii), 5'ss of exon 3
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttt--tcagcgttgaaactatagtaaacatcacttgcagcagtccgaaagagggttagaattgaagctgttccctcaca
|||||||||  | |||||  |||||||||||||| ||||||||||  |||| |||||||| ||||||    |  || | |       |||  ||   | |  | |  ||  ||     |  |   | | | ||  | |  |                         
GTACTTCCTTCGCAAGCTCAAGAAGGTGAAGAAGTCTCACGGCCAGATCCTCGCTATCAACGAGgtaaagttctttctttttctttctttcctcgatgctctagcctta-caagtgagaactttggaacttcgtgacacag-------------------------

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|18333851|gb|BJ165867.1|BJ165867
EST:     CTGCAGAAGGTGAAGAAGGCTCACGGGCCAACTCCTTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: CTGCAGAAGGTGAAGAAGGCTCAC-GGCCAACTCC-TTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|208353060|gb|DC926083.1|DC926083
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37825472|gb|BJ583538.1|BJ583538
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|18346362|gb|BJ178405.1|BJ178405
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37847485|gb|BJ605493.1|BJ605493
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37838414|gb|BJ596422.1|BJ596422
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37852027|gb|BJ610035.1|BJ610035
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37846767|gb|BJ604775.1|BJ604775
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|37822224|gb|BJ580290.1|BJ580290
EST:     AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
EST: gi|208364358|gb|DC950659.1|DC950659
EST:     AGCTGCAGAAGGTGAGGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG                         ATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT
genomic: AGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtgg ... gaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAGgtatgtgtggttgtctgaaaactttttcagcgttgaaactatagtaaacatcacttgcagcagtccgaaagagggttagaattgaagctgttccctcaca

- - - - - - - AGCTGC
- - - - - - - - CTGCAG
- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - AAGAAG