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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggatttgaatgttagtccttatagagaatggtgagaatacacttatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA

Basic information

species Physcomitrella patens
transcript PP1S189_99V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_99V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G157210_T01 (Zea mays), 3'ss of exon 5
--aaggatttgaatgttagtccttatagagaatggtgagaatacacttatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA
       ||   || ||  |  |           ||  |  |  | |  | || | |   | |     ||  || ||||     || || ||||    | ||||| |  |||| |||||| ||||| |  |  | || ||||| ||||| || |||||||||||||| || |||||||| |||||||| |  || |||||  
tttgtccttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaac--ttctcatatggttttggtagGATATTTTGGACTTGGCAAAATATGCATATGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: PP1S189_99V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 2
--aaggatttgaatgttagtccttatagagaatggtgagaatacacttatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA
       ||   || ||  |  |           ||  |  |  | |  | || | |   | |     ||  || ||||     || || ||||    | ||||| | ||||| |||||| ||||| |     | || ||||| ||||| || |||||||||||||| || |||||||| |||||||| |  || |||||  
tttgtccttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaac--ttctcatatggttttggtagGATATTCTGGACTTGGCAAAATATGCATCTGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: PP1S189_99V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G349547_T01 (Zea mays), 3'ss of exon 2
--aaggatttgaatgttagtccttatagagaatggtgagaatacacttatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA
       ||   || ||  |  |           ||  |  |  | |  | || | |   | |     ||  || ||||     || || ||||    | ||||| |  || | |||||| ||||| |     | || ||||| ||||| || |||||||||||||| || |||||||| |||||||| |  || |||||  
tttgttcttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaac--ttctcatatggttttggtagGATATTTTGTACTTGGCAAAATATGCATCTCTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

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|162169624|gb|FC345564.1|FC345564
EST:     TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAG                         GATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT
genomic: TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAGgtgcatcttc ... gtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT
EST: gi|67508196|gb|BJ941067.1|BJ941067
EST:     TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAG                         GATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT
genomic: TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAGgtgcatcttc ... gtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT
EST: gi|162218791|gb|FC394334.1|FC394334
EST:     TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAG                         GATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT
genomic: TACTCTCAGGGTACAACGATGTCATTATGGCGCGTCTCTTCGGACACAAGgtgcatcttc ... gtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA
                          ttctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggatttgaatgttagtccttatagagaatggtgagaatacacttatcttttctatgtaccttgcttaacttctaaaagcgctgatctggtgaatgcagGATCTGCTGGATTTGGCAGAATATTCTAAGATTCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA