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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacatttttggtgctcgctgctttaaggccaataagccgaaacataggttggcacttcgtcattttctaaatcaatctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC

Basic information

species Physcomitrella patens
transcript PP1S36_183V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
gaacatttttggtgctcgctgctttaaggccaataagccgaaa-cataggttggcacttcgtcattttctaaatcaa----tctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC
 |    |||          ||  |  ||   | |      ||  | || | | | |  | |   | ||    | ||     | |   ||  ||| |    | ||||||||||| || || ||||| |||||||||||||| || ||||| |||||  | || ||||| || || || || ||| |||| || ||  |  | ||  
-agggatttacacagatattg--tcgagaatattttatgaaattcctatgcttgaaggttgaagtatttctcaccatgtgtttttttaaaatgtcg--aatgcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 3
gaacatttttggtgctcgctgctttaaggccaataagc--cgaaacataggttggcacttcgtcattttctaaatcaatctcacaatt--tgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC
      | |    ||   ||  |  |   |||| |     | | |     |||   |||   || |||| |   | | |   |   ||  | |   |||| ||||||||||| || || ||||| |||||||||||||| || ||||| || ||||| || || ||||| ||||| || ||| | || |||||  | |||||  
----tctctaaaagcaaacttttggagttccaacagttttctagattatagttcctactagctctttttgtttcttattagtaatgttgttatctatgttacagATGGATGGGTTTGATCAAACAGTGAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTCTGTTGCGTCCTGGTAGACTTGACA

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
gaacatttttggtgctcgctgctttaaggccaataagccgaaacataggttggcacttcgtcattttctaaatcaatctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC
                                                ||        |    |    |||  |   || ||    |  |||| | |||||||||||||||||| ||||| |||||||||||||| |||||||| || || ||||| || ||| | ||||| |||||  | || || ||| | |||||  
------------------------------------------------gtaaaaggaaccgagtagagtaagccg--ctgacgtccttgtgct-tctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

upper sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
gaacatttttggtgctcgctgctttaaggccaataagccgaaacataggttggcacttcgtcattttctaaatcaatctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC
                                                ||        |    |    |||  |   || ||    |  |||| | |||||||||||||||||| ||||| |||||||||||||| |||||||| || || ||||| || ||| | ||||| |||||  | || || ||| | |||||  
------------------------------------------------gtaaaaggaaccaagtagagtaagccg--ctgacgtccttgtgct-tctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

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:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
EST: gi|67696448|gb|BJ956681.1|BJ956681
EST:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
EST: gi|67727787|gb|BJ978046.1|BJ978046
EST:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
EST: gi|162199281|gb|FC375117.1|FC375117
EST:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
EST: gi|162199282|gb|FC375118.1|FC375118
EST:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
EST: gi|162265817|gb|FC442404.1|FC442404
EST:     CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAG                         ATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT
genomic: CTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAAT

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: 12 (upstream exon), 24 (downstream exon)
Score: 1

ATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTGACGCTCAAACTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtataactga ... gctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggttggcacttcgtcattttctaaatcaatctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC
                                              ctgtttc  CT-rich tract
                 attttctaaatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacatttttggtgctcgctgctttaaggccaataagccgaaacataggttggcacttcgtcattttctaaatcaatctcacaatttgttgctgtttcagATGGATGGTTTCGACCAAACTGTGAATGTGAAGGTGATCATGGCCACCAATCGTGCTGATACTCTTGATCCAGCGCTGCTACGACCTGGACGTCTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT