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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtttcatcagtcctcatcgttgtaaaatcagcatatatttagccaagacttagtactctcaagatcttatatctgcatatttcatattacagc...

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 12
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|162187202|gb|FC363152.1|FC363152
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|67699368|gb|BJ959601.1|BJ959601
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|67694426|gb|BJ954659.1|BJ954659
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37851885|gb|BJ609893.1|BJ609893
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|208363930|gb|DC947202.1|DC947202
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37829010|gb|BJ587022.1|BJ587022
EST:     GACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: GACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37831362|gb|BJ589374.1|BJ589374
EST:     AAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|18333101|gb|BJ165115.1|BJ165115
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|162196486|gb|FC375439.1|FC375439
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|162180983|gb|FC358637.1|FC358637
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37827350|gb|BJ585362.1|BJ585362
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37840157|gb|BJ598165.1|BJ598165
EST:     TGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: TGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37844517|gb|BJ602525.1|BJ602525
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|162229880|gb|FC404333.1|FC404333
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|37836338|gb|BJ594346.1|BJ594346
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|162166682|gb|FC342651.1|FC342651
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|208374624|gb|DC948624.1|DC948624
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
EST: gi|18341638|gb|BJ173673.1|BJ173673
EST:     AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG                         AACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG
genomic: AGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAG

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), 32 (downstream exon)
Score: 13

AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtt ... atgactacagAACCTTGATCTGAGCGTGGACTTAAGTGCAGCAAGCGCTGCTGAGGAGTAGAGAGATGGGTGTTTCATACAAGGTATTTTCTCCAGTGGACCAAGGAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAGgttagttgtttcatcagtcctcatcgttgtaaaatcagcatatatttagccaagacttagtactctcaagatcttatatctgcatatttcatattacagc

- - - - - - - - - - - - - - - - - -  AAGATG