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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagcaattcaaatgtatgttatggtctggtctcttcattatctttcagtgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG

Basic information

species Physcomitrella patens
transcript PP1S98_222V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g19150.1 (Oryza sativa), 3'ss of exon 8
------gagcaattcaaatgtatgttatg-gtctggtctcttcattatctttcagtgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG
      | |  |  ||  ||  | ||      || |   |||||| || ||   ||  ||     || | ||||| |||  |  | ||    |  |      ||||||||||||| ||| ||||||| ||||| ||||| |||||||| ||||| ||||||||||  ||| | |||||
aaaatagtgtcaaccagttggcttttgcacaactagaaccttcat-atgttcttgttaaactatttaatatggttttatgctgttttgttttgcaa------tgcagATTGATACAAAAAACATTCTCTTCATTTGTGGTGGTGCTTTTGTTGATTTGGAGAAGACTATTTCGGAAAG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G050186_T05 (Zea mays), 3'ss of exon 8
gagcaattcaaatgtatgttatggtctg-gtctcttcattatctttcag-tgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG
   || | |  || || ||  ||  ||| || |   | || | |  ||    |    |  |   || |||  |    | |     || ||| |    ||||||| ||||||||||| |||||||| |||||||| ||||||||||| || ||||| || |  ||  |||| ||
-cacactgcctat-taagtcttgacctgtgttttggctttttgtcacaaacattgtttagttacttagttccaatggtataatggcatttatgcacatgcagATAGATACCAAAGATATTCTTTTTATATGTGGTGGTGCTTTCGTGGATTTGGAAAAAACTATATCAGAGAG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 8
---gagcaattca-aatgtatgttatggtctggtctct-tcattatctttcagtgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG
   ||  | | ||  |||  | ||  |   ||  || | |  |   |||| |    || |       ||  ||   || || ||    || | | ||   ||||||| ||||||||||| |||||||| |||||||| || |||||||| || |||||||| |  ||  | || ||
aaagaaaattccacgatgcctattgagtcttgacctgtgttttggccttttatcacaaacattgg--ttaattacttaattatg---gcattcatgtacatgcagATAGATACCAAAGATATTCTTTTTATATGTGGTGGCGCTTTCGTGGATTTGGAGAAAACTATATCGGAGAG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G861603_T01 (Zea mays), 3'ss of exon 8
gagcaattcaaatgtatgttatggtctggtctcttcattatctttcagtgtaagctcctactttggt-tgtatatttctgtgaacagttaagtttg--tgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG
     ||||  |  |     ||| | || ||  |      ||  |   |  |  | |         | || | ||||   ||  || ||   ||     |||||||||||||||| ||||||| ||||| || || |||||||| || || |||||||| |  ||| | |||||
--tttattcgtacttgcac-atgttttgatcagtgttcagtcaatagctagacccacaagaaaaaatatgcagattttgatgttcatttgtcttgcatcgcagATTGATACCAAAAACATTCTCTTCATCTGCGGTGGTGCTTTTGTGGACTTGGAGAAAACTATTTCTGAAAG

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|162179889|gb|FC355960.1|FC355960
EST:     ATGTCCCAGAGAAAGGGGCACGGAAACATCCAAGAGGAGAACACATTCAG                         ATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTG
genomic: ATGTCCCAGAGAAAGGGGCACGGAAACATCCAAGAGGAGAACACATTCAGgtactgtgtt ... gtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTG
EST: gi|162247501|gb|FC425067.1|FC425067
EST:     ATGTCCCAGAGAAAGGGGCACGGAAACATCCAAGAGGAGAACACATTCAG                         ATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTG
genomic: ATGTCCCAGAGAAAGGGGCACGGAAACATCCAAGAGGAGAACACATTCAGgtactgtgtt ... gtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG
                     ttgtatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagcaattcaaatgtatgttatggtctggtctcttcattatctttcagtgtaagctcctactttggttgtatatttctgtgaacagttaagtttgtgcagATTGATACCAAAGACATTCTTTTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA