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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGAGCAGATTGCTGGCCGAGATAACATTTTGAACCATAATAGCGTGCCCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggtcctgttgttttagaagctatcgtggcagtgccttagttttggatcttcttgtgatgttattggcatggctcaaggcccttagtccatttcctattctggtaagaacggatttctttttatttctttgcag

Basic information

species Physcomitrella patens
transcript PP1S35_94V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 11
AATTGAGCAGATTGCTGGCCGAGATAACATTTTGAACCATAATAGCGTGCCCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtaca-gtggtcctgttgttttagaagctatcgtggcagtgccttagttttggatcttcttg-tgatgtta-ttggcatggctcaaggcccttagtccatt-tcctattctggtaagaacggatttctttttatttctttgcag-----------------------------------------
  | ||||| ||   |||  | || |||||||| || ||    ||| | || || || |||||||| |||||||||||||| |||||||||||||| ||||||   | | | |  || |   | |    ||  |        | |||||    |||| |||| | | |||| || |  | |  ||    | | |||  |   ||  |   || |   |||    ||  |||  ||   | |||                                          
TGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgagataccattctccaatattacattctctgttcaacatagttg-aaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaact--cttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcag

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 6
AATTGAGCAGATTGCTGGCCGAGATAACATTTTGAACCATAATAGCGTGCCCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtg-gtcctgttgttttagaagct--atcgtggcagtgccttagttttggatcttcttgtgatgttattggcatggctcaagg-cccttagtccatttcctattctggtaagaacggatttctttttatttctttgcag
  |||| ||  |  ||||  ||||| || |  | || |||   ||| | || || || |||||||| || ||||| |||||||||||||| |||||||||||| |     |  | || |  | || | |   ||    |     |  | |  || || || |  |  |  | |   ||||||| |  | |||||  ||  |                                           
GGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGAGgtatatcatattttcttttcgttgatgtttcttctcttcctccacccactgctgcatgtt-tcattcttctgtgcacatggctaactgtcccttcctctgt-------------------------------------------
















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|162239089|gb|FC416228.1|FC416228
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|19786466|gb|BQ040483.1|BQ040483
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|67692532|gb|BJ952765.1|BJ952765
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162195483|gb|FC370900.1|FC370900
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTT
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTT
EST: gi|162195482|gb|FC370899.1|FC370899
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162185503|gb|FC362572.1|FC362572
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162185502|gb|FC362571.1|FC362571
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162167618|gb|FC343750.1|FC343750
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162170368|gb|FC346773.1|FC346773
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|208380575|gb|DC919361.1|DC919361
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162166908|gb|FC343293.1|FC343293
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
EST: gi|162239088|gb|FC416227.1|FC416227
EST:     CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAG                         CCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA
genomic: CCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggt ... ttctttgcagCCACAAGCAAGAGCGTTGGGAACGGAAGAGGGTTTCAAAGTAAGCGTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGAGCAGATTGCTGGCCGAGATAACATTTTGAACCATAATAGCGTGCCCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGAGgtacagtggtcctgttgttttagaagctatcgtggcagtgccttagttttggatcttcttgtgatgttattggcatggctcaaggcccttagtccatttcctattctggtaagaacggatttctttttatttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA