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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataaattctttatgtattacatattcgtctgagaactgaaattcacatatctgtttgagtttggtcatgtttttagctaatcagttcttcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG

Basic information

species Physcomitrella patens
transcript PP1S68_29V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_29V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 3
atataaattctttatgtattacata-ttcgtctgagaactgaaattcacatatc-tgtttgagtttg-gtcatgtttttagctaatcagttcttcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG-----
  || ||  |||    |  || ||| |||    |     || |||     | |  |||||   |||  |||||||  ||    ||||| |   |    || || ||  | ||||| || ||   ||| |||||||| || || ||||| ||  | ||  ||||||||||||||||||||||||| || || || || |     
-gatgaacactt-gcatgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattc-taaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
















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|100390452|gb|BY952860.1|BY952860
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|208362530|gb|DC931007.1|DC931007
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|208374670|gb|DC931995.1|DC931995
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|162264779|gb|FC440346.1|FC440346
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|18363082|gb|BJ195154.1|BJ195154
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|162209020|gb|FC385572.1|FC385572
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|162209019|gb|FC385571.1|FC385571
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|162264778|gb|FC440345.1|FC440345
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|208387224|gb|DC945523.1|DC945523
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|18329923|gb|BJ161929.1|BJ161929
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
EST: gi|208358537|gb|DC946498.1|DC946498
EST:     GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAG                         GGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT
genomic: GCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTT

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: 27 (upstream exon), 17 (downstream exon)
Score: 7

ATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGGATGCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATACTAGgtatgctttt ... tcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatatctgtttgagtttggtcatgtttttagctaatcagttcttcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG
                               agctaat  putative branch site (score: 7)
                                         ttcttc  putative PPT
                       atgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataaattctttatgtattacatattcgtctgagaactgaaattcacatatctgtttgagtttggtcatgtttttagctaatcagttcttcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT