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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG

Basic information

species Physcomitrella patens
transcript PP1S38_137V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
attggagggtacata---aggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
     | | | | |    | |||  | || | |||  |  |       | |   || ||         ||       | |     |  |    |  ||||||||||| |||||||||||| | || ||| | ||  ||||| |||||||||| || || || || || ||||||||||| || ||||||||||| || || ||
--ccaatgtttcttggctacgatttatttcg-attatataacttccatgaaaaaatttccagaaaacgattgatatgcttctgaattattgtttacattgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 2
----attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
     ||    ||| |   |   |     ||  || | | |  |||    |   | || |  |  |    |   |||     |   ||   |  ||  |||||||||| |||||| ||||| |||| ||| | ||  ||||  |||||||||| || || || ||||| ||||||||||||||||||||||| || || || ||
cgaactttcctggtcctggattcttttaattagatagcatggaagaa--aggatcttgacaaaaag-acctagaatcttaaggttttgacgttttgt-ttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
-attggagggtacataag-gatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgc--agAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
  ||||    |    ||   |  ||     | || ||    |||  | ||  ||   || |   |   | |    |  ||    |  |||  ||  ||||  ||||||||| ||||| ||| | || ||  | ||  ||||| ||||||||||||| || || || || ||||||||||||||||| ||||| || || || ||
tcttggttcattttcaattaaagcaagccattttagattt-agagcctgaaaca-accgcaa-ataccttattcgaaatattattt-tcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G05940.2 (Glycine max), 3'ss of exon 2
attggagggtacataaggatccagtttgtattggaagagagattcggaggca-tgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
 ||    | |       || |  |||   | || ||| ||| | |   |  | | |  |   |  |      |      |  ||| | |  |      |||| ||||| ||| | ||||||||||| |||||  |||||  ||||||||| |||||||| || ||||| |||||||| || ||||| || |||||  | ||
gttaattgatgagagtagagcacgttaacaatgcaagtgaggtacactgataatatactgatgcttcatttgtttaactgttgtg-tttattttgcaccagAAAAGGATAATCTTTGTCTGTACGGATTCCCTAATGAGCAATGGGAAGTTAATTTACCTGCGGAAGAAGTTCCTCCGGAGCTTCCTGAGCCTGCATTGGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G26210.1 (Arabidopsis thaliana), 3'ss of exon 2
attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctg-aattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
  | |||  |       |    ||| |  |||    |   || | ||    |  |    |  | |   |||      | |  |   ||  ||  |||  ||| ||||||||  | || || |||||    ||  |||||   |||||||| ||||| ||||| ||||||||||||||||| || ||||| |||| | | ||
-gtagagtttgagcggagtcaaagtgttgattttttgtttgacttggttttaatttaaggttttttgaacaattgtcatcattttccttttgtgattatagAAAAGGAGAACCTTTGCCTTTACGGACATCCAAATGAGCACTGGGAAGTGAATTTGCCAGCTGAAGAGGTTCCTCCTGAGCTCCCAGAGCCTGTCTTGGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
--attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
    |    ||||    |  ||    ||| || |   ||     ||  | ||    | |      ||      |   |||  | |    |   |  || |||||||||||||| | ||  |||| || || ||| |||| | ||||||||| ||||||||||| ||||| || ||||||||  | ||||| || || |||||
gtggttattggtattgtacaatatgatttatactt--agtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG

upper sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv09s0002g01600.t01 (Vitis vinifera), 3'ss of exon 2
-attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG
 |  | |   |   |  |     || |  |   |          | | |||| || | |      | | |  |    ||   ||  | |||    || |||||||||||||| |||| || || || || ||  ||||   ||||||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||
tacagaatcttgtttcggatatgagatattccagctcttattcctagaaggcctgccttctatgattttaacttggctacatgtattttgc-accttacagAGAAGGAGAATCTGTGCCTTTATGGATTTCCAAATGAACTATGGGAAGTCAATTTACCTGCAGAAGAGGTGCCTCCAGAACTCCCAGAGCCTGCACTAGG

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|208386803|gb|DC937195.1|DC937195
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100402332|gb|BY954783.1|BY954783
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAA                         AGA-GGAGGATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|208392532|gb|DC938525.1|DC938525
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100409328|gb|BY991957.1|BY991957
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGGAAGTA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGG-AAGTA
EST: gi|100437784|gb|BY979826.1|BY979826
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAAGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100409548|gb|BY955987.1|BY955987
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGA-TTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAG
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAG
EST: gi|100424056|gb|BY976643.1|BY976643
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100443763|gb|BY963860.1|BY963860
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGG-GGNAGAATTTGTGTCTGTACGGTTTTCCGGGATGAGGCATGGGAAGT
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGG-AGAATTTGTGTCTGTACGGTTTCCCGG-ATGAGGCATGGGAAGT
EST: gi|208392010|gb|DC941858.1|DC941858
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|208347209|gb|DC957474.1|DC957474
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|208352865|gb|DC910084.1|DC910084
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAN                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGANGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100378832|gb|BY968711.1|BY968711
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100370773|gb|BY948509.1|BY948509
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
EST: gi|100432760|gb|BY978734.1|BY978734
EST:     ATGTTGAAGACTTTTACCGCCAGTGTGATCCAG                         AGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA
genomic: ATGTTGAAGACTTTTACCGCCAGTGTGATCCAGgtgcgaaatt ... tgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG