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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgcattcgaatatgttgattttgagattagcggatttgaggttcttaatccctcgtaatttagcagcagaatgctaatgtagtccatggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACGAAGTTCTCGTCTATCGCTTCAAGTTTTATTGCAGATCTACAGGATCGCA

Basic information

species Physcomitrella patens
transcript PP1S795_4V6.2
intron # 7
splice site 3'
intron type U2

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|208370166|gb|DC951765.1|DC951765
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAAGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|208368245|gb|DC951511.1|DC951511
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|208358641|gb|DC949976.1|DC949976
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|67696742|gb|BJ956975.1|BJ956975
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|208396541|gb|DC915853.1|DC915853
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|162221477|gb|FC397286.1|FC397286
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|67720059|gb|BJ970318.1|BJ970318
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|208362683|gb|DC947174.1|DC947174
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|162200943|gb|FC377346.1|FC377346
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|67695640|gb|BJ955873.1|BJ955873
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|67698195|gb|BJ958428.1|BJ958428
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|18334153|gb|BJ166169.1|BJ166169
EST:     CTTCTATTGACGTTACGTCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|162194335|gb|FC368518.1|FC368518
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|67572272|gb|BJ945096.1|BJ945096
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|37830194|gb|BJ588206.1|BJ588206
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|18335952|gb|BJ167973.1|BJ167973
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|18335829|gb|BJ167850.1|BJ167850
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
EST: gi|37823009|gb|BJ581075.1|BJ581075
EST:     CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAG                         GCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG
genomic: CTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTAAACTCACATACCAGgtaatagaga ... ggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaatccctcgtaatttagcagcagaatgctaatgtagtccatggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACGAAGTTCTCGTCTATCGCTTCAAGTTTTATTGCAGATCTACAGGATCGCA
                             tgctaat  putative branch site (score: 2)
             taattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcattcgaatatgttgattttgagattagcggatttgaggttcttaatccctcgtaatttagcagcagaatgctaatgtagtccatggttgttcagGCCTCGCAGGATATTTCAGCCTTAAAAAACATGGCAGGAGAAACTGCCACGAAGTTCTCGTCTATCGCTTCAAGTTTTATTGCAGATCTACAGGATCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT