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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaaagcttagtcataggatagctgttcagttctttgtatcgtattttcagtccatttttcttatgctttctgaaggaatccttatgttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG

Basic information

species Physcomitrella patens
transcript PP1S460_22V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S460_22V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os08g07850.1 (Oryza sativa), 3'ss of exon 7
--attaaagcttagtcataggatagctgttcagttctttgtatcgtatt-ttcagtccatttttcttatgctttctgaaggaatcc-ttatgttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG
  ||||   || |   ||     || | ||   || || |  | ||  | |   ||  || |   || |  ||| |   | | |   |||| ||| |  |||||||||||||||||||||| || ||  | |||||||| || ||||| ||||| || ||||| || || | |||  |||| ||||||||||| || 
ttattacttctgacaaatgcatcagttttt--attgttagagtggtgctatatcgtttatgtaaattttatttttttttgaactaagttatcttcct--tgcagAATCAACCTGCTCTTGAAAAGGATAGGTACAAGATTCGCCAAGCTTTTGTCGCAGCTCCAGGGAACACTCTTATTGTTGCTGATTATGGCCAA

upper sequence: PP1S460_22V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA02G45910.1 (Glycine max), 3'ss of exon 6
attaaagcttagtcataggatagctgt-tcagttctttgtatcgtattttcagtccatttttctta-tgctttctgaaggaatccttatg-ttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG
    ||  |   |  |   ||   | | | |||  |   |||  ||  || | ||    ||||  |  | |||   |   ||  | ||   ||| |||   |||||||||||||||| || || ||||| ||||| ||||||||||||||  ||||||| ||||| ||   |||  | || |||||||||||||||
---caatttgtattttgacattcatatgtgagtaatacatatactagatttaatcagactttcaaaacgatttagaacctaacacatacacttcatgaattagAATCAACCTGCTCTGGAAAAGGACCGATACAAAATCCGTCAAGCATTCATTGCTGCACCTGGGAATTCTCTTATAGTTGCTGATTATGGACAG

upper sequence: PP1S460_22V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G04810.1 (Glycine max), 3'ss of exon 5
attaaagcttagtcataggatagctgttcagttctt-tgtatcgtattttcagtccatttttcttatgctttctgaaggaatccttatg-ttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG
  | ||  |   |  |   || |   | | | | ||   |    ||  || |    | |||    |   | |   |    |  |||| | ||| |||   |||||||||||||||| || || || || ||||| ||||||||||||||  ||||||| ||    ||   |||  | || |||||||||||||||
--tcaatttgtattttgacattgacatgcgggtattacatccactagattaatcagactttcaaaacaatatagaacctgacacttacgcttcatgaattagAATCAACCTGCTCTAGAAAAGGATCGATACAAAATCCGTCAAGCATTCATTGCTGCACCCAAGAATTCTCTTATAGTTGCTGATTATGGACAG

upper sequence: PP1S460_22V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA14G02860.1 (Glycine max), 3'ss of exon 9
attaaagcttagtcataggatagctgttcagttctt-tgtatcgtattttcagtccatttttcttatgctttctgaaggaatccttatg-ttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG
  | ||  |   |  |   || |   | | | | ||   |    ||  || |    | |||    |   | |   |    |  |||| | ||| |||   |||||||||||||||| || || || || ||||| ||||||||||||||  ||||||| ||  | ||   |||  | || |||||||||||||||
--tcaatttgtattttgacattgacatgcgggtattacatccactagattaatcagactttcaaaacaatatagaacctgacacttacgcttcatgaattagAATCAACCTGCTCTAGAAAAGGATCGATACAAAATCCGTCAAGCATTCATTGCTGCACCCAGGAATTCTCTTATAGTTGCTGATTATGGACAG

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|162159256|gb|FC335109.1|FC335109
EST:     ATATCAACACTGAAACTGGGCGTTTGTCTGCAAGAAGACCAAGTCTGCAG                         AATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTT
genomic: ATATCAACACTGAAACTGGGCGTTTGTCTGCAAGAAGACCAAGTCTGCAGgtcggtgttt ... cttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTT




















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-Seq library.


Block sizes: 35 (upstream exon), 28 (downstream exon)
Score: 2

GGTAATGATATTAAGAGTGCTTCCGATGGACGTGTACACTGTTCCTTGAATATCAACACTGAAACTGGGCGTTTGTCTGCAAGAAGACCAAGTCTGCAGgtcggtgttt ... cttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcagtccatttttcttatgctttctgaaggaatccttatgttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG
                                            tcttgat  putative branch site (score: 2)
                                         tgttctt  CT-rich tract
          atttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaaagcttagtcataggatagctgttcagttctttgtatcgtattttcagtccatttttcttatgctttctgaaggaatccttatgttcttgatgcagAATCAACCTGCTCTTGAGAAAGACCGCTACAAGATCCGTCAAGCATTTGTTGCTGCTCCTGGAAAGAGTCTAGTTGTGGCTGATTATGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT