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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCCTAATTTCAAGTGCAATCTTCTTCCGGGGGGAGTGATGGTGTTGTGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttttctacgatcgttttctgaataggtgtgcaattggactcctctttgcgttttcgattctgcggttgcgtgatattcgcgaagtttacactt...

Basic information

species Physcomitrella patens
transcript PP1S78_51V6.3
intron # 1
splice site 5'
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|208350208|gb|DC901592.1|DC901592
EST:     GACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: GACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|162223284|gb|FC400552.1|FC400552
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100438163|gb|BY961685.1|BY961685
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100366190|gb|BY967324.1|BY967324
EST:     ACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: ACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18327728|gb|BJ159731.1|BJ159731
EST:     CTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208389023|gb|DC937356.1|DC937356
EST:     CGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208357565|gb|DC934073.1|DC934073
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGGAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100406166|gb|BY991572.1|BY991572
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100416027|gb|BY957042.1|BY957042
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208374347|gb|DC941160.1|DC941160
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18367012|gb|BJ199092.1|BJ199092
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208345657|gb|DC909588.1|DC909588
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100447063|gb|CJ971362.1|CJ971362
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|162259610|gb|FC436473.1|FC436473
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208345181|gb|DC909487.1|DC909487
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAANAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|162173089|gb|FC349195.1|FC349195
EST:     GATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: GATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100444657|gb|BY982486.1|BY982486
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|67569551|gb|BJ942375.1|BJ942375
EST:     GCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: GCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18348373|gb|BJ180421.1|BJ180421
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100445538|gb|CJ975687.1|CJ975687
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTANAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18373429|gb|BJ205007.1|BJ205007
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18326047|gb|BJ158046.1|BJ158046
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|162272333|gb|FC449011.1|FC449011
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18327748|gb|BJ159751.1|BJ159751
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18328785|gb|BJ160790.1|BJ160790
EST:     TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAG                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: TGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG

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: 23

GAGACCCTAATTTCAAGTGCAATCTTCTTCCGGGGGGAGTGATGGTGTTGTGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttt ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCGTGTTGCGCATCATGCGCATGCTCGGCATGTCAGGGGGTAGCAAGTGGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACCCTAATTTCAAGTGCAATCTTCTTCCGGGGGGAGTGATGGTGTTGTGACTTTGCGGCAGATTGTTGGATCGATTGTTGGGGGACAATTGCAACAGgttagacttttctacgatcgttttctgaataggtgtgcaattggactcctctttgcgttttcgattctgcggttgcgtgatattcgcgaagtttacactt

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