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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagattattacctgttcttttgcttaagtattcaagtgaattgatggagtcagttgctattgctacggaaatgagctgaaacactaagcttgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGGACAACAGGTTCTGGCTTAGAAGGCCCATCTTATCCAATGGAGGAGGCTG

Basic information

species Physcomitrella patens
transcript PP1S41_313V6.1
intron # 2
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|162242370|gb|FC416126.1|FC416126
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162255371|gb|FC432097.1|FC432097
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162268052|gb|FC443522.1|FC443522
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|19778728|gb|BQ039350.1|BQ039350
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTG
EST: gi|162225323|gb|FC400841.1|FC400841
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|100416872|gb|BY993131.1|BY993131
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|100394920|gb|BY989991.1|BY989991
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162219476|gb|FC396954.1|FC396954
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|100406705|gb|BY955703.1|BY955703
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162225322|gb|FC400840.1|FC400840
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162230598|gb|FC407461.1|FC407461
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|208395960|gb|DC915720.1|DC915720
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162236522|gb|FC413097.1|FC413097
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162268053|gb|FC443523.1|FC443523
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|208371538|gb|DC936259.1|DC936259
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAGCAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67698881|gb|BJ959114.1|BJ959114
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67573226|gb|BJ946050.1|BJ946050
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162236523|gb|FC413098.1|FC413098
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67696780|gb|BJ957013.1|BJ957013
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67573399|gb|BJ946223.1|BJ946223
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|18338317|gb|BJ170341.1|BJ170341
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162228314|gb|FC404068.1|FC404068
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|37824838|gb|BJ582904.1|BJ582904
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|208360491|gb|DC950065.1|DC950065
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAGCAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67578152|gb|BJ950319.1|BJ950319
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162255370|gb|FC432096.1|FC432096
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162228315|gb|FC404069.1|FC404069
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162242371|gb|FC416127.1|FC416127
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67696610|gb|BJ956843.1|BJ956843
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162230599|gb|FC407462.1|FC407462
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|100444973|gb|BY982801.1|BY982801
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|67575414|gb|BJ948238.1|BJ948238
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|208363770|gb|DC931094.1|DC931094
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|208388333|gb|DC945609.1|DC945609
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|37827288|gb|BJ585300.1|BJ585300
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
EST: gi|162219477|gb|FC396955.1|FC396955
EST:     GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAG                         GATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG
genomic: GTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 34 (downstream exon)
Score: 45

TGAGGTCTCTCCTGATTCCCTGGACAAAGAGGAGATTTCTCCTGAGGCAGGTGCTATTGTTGTGTCGTCGTTGTCTACATCTTTGCAGACCCTATCGAAGgtgagttgaa ... tgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGGACAACAGGTTCTGGCTTAGAAGGCCCATCTTATCCAATGGAGGAGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtcagttgctattgctacggaaatgagctgaaacactaagcttgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGGACAACAGGTTCTGGCTTAGAAGGCCCATCTTATCCAATGGAGGAGGCTG
                                          gcttgat  putative branch site (score: 45)
                                            ttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagattattacctgttcttttgcttaagtattcaagtgaattgatggagtcagttgctattgctacggaaatgagctgaaacactaagcttgatttacagGATGAGGCAATGGGAATCATTTTGAATGCCGCTGGGTCAACAGCTGGTTGGACAACAGGTTCTGGCTTAGAAGGCCCATCTTATCCAATGGAGGAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG