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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcag

Basic information

species Physcomitrella patens
transcript PP1S62_136V6.1
intron # 3
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|162224578|gb|FC400474.1|FC400474
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18356528|gb|BJ188587.1|BJ188587
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67724058|gb|BJ974317.1|BJ974317
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67699838|gb|BJ960071.1|BJ960071
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18358209|gb|BJ190268.1|BJ190268
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67709980|gb|BJ965796.1|BJ965796
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37837576|gb|BJ595584.1|BJ595584
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67716706|gb|BJ966966.1|BJ966966
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67576322|gb|BJ949146.1|BJ949146
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37833438|gb|BJ591450.1|BJ591450
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|162259896|gb|FC436031.1|FC436031
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37827014|gb|BJ585026.1|BJ585026
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37827815|gb|BJ585827.1|BJ585827
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|15261763|gb|BI437073.1|BI437073
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGTCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37853590|gb|BJ611598.1|BJ611598
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|13250705|gb|BG361608.1|BG361608
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37833460|gb|BJ591472.1|BJ591472
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18357240|gb|BJ189299.1|BJ189299
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37836608|gb|BJ594616.1|BJ594616
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|13251050|gb|BG361944.1|BG361944
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGAGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67725227|gb|BJ975486.1|BJ975486
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18339625|gb|BJ171652.1|BJ171652
EST:     NCAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCNCTGGACCGATCGGNAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|37841274|gb|BJ599282.1|BJ599282
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|162225990|gb|FC400995.1|FC400995
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|162224577|gb|FC400473.1|FC400473
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18347608|gb|BJ179655.1|BJ179655
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|162225989|gb|FC400994.1|FC400994
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67695515|gb|BJ955748.1|BJ955748
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18356504|gb|BJ188563.1|BJ188563
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|7648252|gb|AW739235.1|AW739235
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTGTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAAACTGGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|67709636|gb|BJ965452.1|BJ965452
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18364186|gb|BJ196259.1|BJ196259
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCG
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAA-GGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCG
EST: gi|67723711|gb|BJ973970.1|BJ973970
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|18360226|gb|BJ192288.1|BJ192288
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCG
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAA-GGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCG
EST: gi|67572147|gb|BJ944971.1|BJ944971
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
EST: gi|15729024|gb|BI741098.1|BI741098
EST:     ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG                         GTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA
genomic: ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGA

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: 35 (upstream exon), 35 (downstream exon)
Score: 69

ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcag

-  ATGCTG
- - - - - - - - - - - - - -  GGAGAA