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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttcaacactgagcattactgtgcttcgcctcaacctttgtaattgttgtctgtcggtttggaatcgaatggtttctagacttttgttttgtactttcaatatgctcaatgagacggttctgaagattaacgttaattttcatatgttgcgtag

Basic information

species Physcomitrella patens
transcript PP1S33_211V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GRMZM2G065494_T01 (Zea mays), 5'ss of exon 13
GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttcaacactgagcattactgtgcttcgcctcaacctttgtaattgttgtctgtcggtttggaatcgaatggtttctagacttttgttttgtactttcaatatgctcaatgagacggttctgaagattaacgttaattttcatatgttgcgtag
 | ||||| ||||||||||| ||||| |||||||| ||||||||| |||||| |  ||| |         ||| | | |||     | ||||     |          |       ||  ||    || |  |                                                                          
CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatg-caata---------actttccgtcgtgctgatctttacttataaaacaaactgaagaaacataaaactcattttgcag-------------------------------------------------------------------------
















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|208359001|gb|DC957749.1|DC957749
EST:     GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTC                         GTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
genomic: GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttc ... tgttgcgtagGTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
EST: gi|162252971|gb|FC429032.1|FC429032
EST:     GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTC                         GTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
genomic: GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttc ... tgttgcgtagGTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
EST: gi|162252972|gb|FC429033.1|FC429033
EST:     GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTC                         GTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
genomic: GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttc ... tgttgcgtagGTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
EST: gi|67725482|gb|BJ975741.1|BJ975741
EST:     CATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGANTACTC                         GTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA
genomic: CATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttc ... tgttgcgtagGTATGTCGAATGCACGTCAGCGTGCATGCAAGCGCTCGCTTCTTTTCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTCgtaagttttcaacactgagcattactgtgcttcgcctcaacctttgtaattgttgtctgtcggtttggaatcgaatggtttctagacttttgttttgtactttcaatatgctcaatgagacggttctgaagattaacgttaattttcatatgttgcgtag

- - - - - - - - - - - TTGGAG
- - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - GGAGAT