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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagaatttctattttagagggggtgttttgtgttcgctgtctagtactcattgcattcggcttgtcagagtatttaacttggattctggaaccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG

Basic information

species Physcomitrella patens
transcript PP1S80_144V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------gtactagaatttctattttagagggggtgttttgtgttcgctgtctagt---actcattgcattcggcttgtcagagtatttaacttggattctggaa-------ccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG
                                                                              | |   |||  || |||     |      || |    |   | |  |     | ||| |||   | |   | ||     | | | | ||| |   |       ||| ||||||| | ||| || ||||| || || ||||| ||||| ||||| ||  ||||||||||||| ||||| ||||| |||||||| ||  | || |||||||| |
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG

upper sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 7
gtactagaatttctattttagagggggtgttttgtgttcgctgtctagtactcatt----gcattcggcttgtcagagtatttaacttggattctggaaccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG
          || |||  | |  |     |||||  || ||| |  | |  |  |        ||   | |  ||   |  |||   |   || |  | |   |||||||||||||| | || || |||||  |||| ||||| ||||||||| |||||||||| ||||| |||||||| |||||||| ||| | || ||||||||  
------cttcttttatcct-gttgcatcattttgc-ttggcttttgaatttttttctttaatttttaaccttgcaatttcattagtatttgttttccatcttctgcagTACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCTTTTTCAT

upper sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 7
gtactagaatttctattttagagggggtgttttgtgttcgctgtctagtactcattgcattcggcttgtcagagtatttaacttggattctggaaccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG-
     ||    || ||  | |  |||   || | | || |   | |  |  | | |   ||   |||  || | |  |||   |   || |    |   |||||||||||||| | || || |||||  |||| ||||| ||||||||| |||||||||| ||||| |||||||| |||||||| ||| | || || |||||   
---gaaggtcctccatcattgcagggcatttgtatttttgtatttttatctttaatt--tttaactttgcaaattcattattatttgttttctgtcttctgcagtACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCCTTTTCATT

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|162169925|gb|FC345865.1|FC345865
EST:     CAATTCCTGACGGAGGTCACTTTACTGTTTGCGGTGATATTCATGGGCAG                         TACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAG
genomic: CAATTCCTGACGGAGGTCACTTTACTGTTTGCGGTGATATTCATGGGCAGgtactagaat ... accaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAG




















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: 30 (upstream exon), 19 (downstream exon)
Score: 2

TTTGAAAACGCGAGAGCTATTGTTAGCAACGCCTACTTTGGTTCACATTGCAATTCCTGACGGAGGTCACTTTACTGTTTGCGGTGATATTCATGGGCAGgtactagaat ... accaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcattgcattcggcttgtcagagtatttaacttggattctggaaccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG
                          atttaac  putative branch site (score: 2)
                         tatttaactt  TA-rich tract