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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctttttttatttgaccggaattgttgtgaatgtatttaggtcattgtttgtttgaattattagtgcttgagagttagtagtcttgtgaatttcggtctttcgatccttaccttcttgttttcgattgtttattttgtcaaag

Basic information

species Physcomitrella patens
transcript PP1S2_217V6.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 5'ss of exon 19
GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgt------tcgggctttttttatttgaccggaattgttgtgaatgtatttaggtcattgtttgtttgaattattagtgcttgagagttagtagtcttgtgaatttcggtctttcgatccttaccttcttgttttcgattgtttattttgtcaaag
|| || || |||||  ||||||||||| | ||||| ||||||||| |||||||||||||      |     |||  ||||||    | | | ||  |         |   | ||  ||| || |  | |    ||   |                                                                         
GTTGTCCCGGAGACTCTGGAGCCTAGTCTACAGTTGGCAGCTGCTGTTCTTGCTCAGgtaaaacataaatgtttccttatttagttgaagtagtaatcctaaacagtgtatgatcattttttgggttgaaacatgtcag-------------------------------------------------------------------------
















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|162256773|gb|FC432667.1|FC432667
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162178087|gb|FC354389.1|FC354389
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162167759|gb|FC344073.1|FC344073
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162174994|gb|FC350893.1|FC350893
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162174995|gb|FC350894.1|FC350894
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162191638|gb|FC367683.1|FC367683
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
EST: gi|162178086|gb|FC354388.1|FC354388
EST:     CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG                         GCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC
genomic: CAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctt ... tttgtcaaagGCTAAATTACCAGCATCAGAGATCGCTGCGGCAATTGACCAGTTCCGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAGgttcgggctttttttatttgaccggaattgttgtgaatgtatttaggtcattgtttgtttgaattattagtgcttgagagttagtagtcttgtgaatttcggtctttcgatccttaccttcttgttttcgattgtttattttgtcaaag

- - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - -  GCTGCT