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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcgtctttttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaaagattat...

Basic information

species Physcomitrella patens
transcript PP1S36_183V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 5'ss of exon 2
GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcgtctttttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaa-agattat-
 || || ||||| ||||||||||| || ||||| |||||||| ||||| ||||| ||  | || |||||||| |||||||||||||||||  | || ||||||| |     || | |   |  |||  ||||   | |   || || ||    | | |||| ||  |  |    | ||   || ||   ||   || |  | 
TACTGGCAAGACCATGCTTGCCAAAGCAGTCGCACATCATACCACCGCTGCTTTTATCAGAGTCGTTGGTTCGGAGTTTGTACAGAAGTACTTGGGCGAGgtaa-gttgggacatgggagctattataatgccaatatgaatt-cttttggattggatataaaatgtagtgaattcataggtatggcgttgcctaggtcctg

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 2
-GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcgtctttt-tcttgctattcctgttgttatagaaactgt--ttgtctgatttataaggtcatgaaagattat--
  || || || || ||||||||||| ||||| ||  ||||||| || || ||||||||  | ||||| || ||||||||||| |||||||||||||| ||||||      | | ||| ||| | |  ||||  |  | |  | |||  | |  ||| | |       || |  |||| |  |||  ||  | |||       |   
GCACTGGCAAAACAATGCTTGCCAAAGCTGTTGCGAATCATACCACTGCTGCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggta------tcatttttatatcatctgcatatggatgtgatgttgacaatgttgtagcttactctgctatctttgtttctttttgaaaattatgggtttccaatt

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G31450.1 (Glycine max), 5'ss of exon 2
GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcgtcttt-------ttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaaagattat
 || ||||| || ||||||||||| ||||| ||  ||||||| || || || |||||  | ||||| || ||||||||||| |||||||||||||| |||||| ||   |||  |      | || | |||||   ||       || | |||    ||| | |  |||   || ||||    | ||||  | |    |   |    
CACTGGAAAAACAATGCTTGCCAAAGCTGTTGCGAATCATACCACTGCCGCCTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAGgta-tgattttaagtcatctgcatttggatgcgatgttgacaatgttgtagcttactctgctatcttagtttctttttga--aaattatgggtttccaattca----

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G31470.1 (Glycine max), 5'ss of exon 2
GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcg-tctttttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaaagattat---
 || || || || ||||||||||| ||||| ||| ||||||| || || || |||||  | ||||| || ||||||||||| || ||||||||||| ||||||      |||  |      | || | ||||| | ||     || | |  ||  |  | |   | ||  |||| |  |||  ||  | |||       |    
CACTGGCAAAACAATGCTTGCCAAAGCTGTTGCTAATCATACCACTGCCGCCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAGgtatgatttttaagtcatcttcatttggatgcgatgttgacaatgttgtaact--tactctgctatct--ttgtttctttttgaaaattatgggtttccaattc

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ04233 (Selaginella moellendorffii), 5'ss of exon 2
GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatg---ccattactttgatacccttagcatgcgtctttttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaaagattat
 || || || || |||||||| ||||| ||||| || || || || || |||||||| || ||||| || || ||||| || |||||||||||||| |||||   |   |  ||  |||      ||   || || | | ||   ||  |                                                     
CACTGGGAAAACCATGCTTGCAAAGGCCGTCGCGCACCACACCACTGCCGCTTTCATCCGCGTTGTGGGCTCGGAGTTCGTCCAGAAGTATCTTGGAGAGgtgtggaaccttttcttttttctttctcttcacgcttgtcttctgtggcacag--------------------------------------------------

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|162265816|gb|FC442403.1|FC442403
EST:     CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAG                         GGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
genomic: CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
EST: gi|67727787|gb|BJ978046.1|BJ978046
EST:     CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAG                         GGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
genomic: CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
EST: gi|162199281|gb|FC375117.1|FC375117
EST:     ATCTTGGGGAG                         GGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
genomic: ATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
EST: gi|162199282|gb|FC375118.1|FC375118
EST:     ATCTTGGGGAG                         GGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
genomic: ATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
EST: gi|162265817|gb|FC442404.1|FC442404
EST:     CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAG                         GGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA
genomic: CTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCA

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: 9 (upstream exon), 35 (downstream exon)
Score: 2

GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccat ... cttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCAGCCATTATATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAGGAAAGACTATGCTTGCCAAGGCTGTCGCTCATCATACTACCGCAGCTTTCATTCGTGTTGTTGGTTCTGAGTTTGTACAGAAGTATCTTGGGGAGgtaatgccattactttgatacccttagcatgcgtctttttcttgctattcctgttgttatagaaactgtttgtctgatttataaggtcatgaaagattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT