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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcatccaaaaacctactcataatgatttgaatgcaatttacatgtagttcacgtgagaaattcacatatgcggctgttttggaaggctcagtaccatgaagattatcatgcattgccataaaatttgcaatttttttgactgagtcatgacgtgtcaggagtacattgatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTACCTGGGGAATCCAAGGTCATCCTAGTTGCATACGCAAACAG

Basic information

species Physcomitrella patens
transcript PP1S89_217V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S89_217V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 5
gtactttcatccaaaaacctactcataatgatttgaatgcaatttacatgtagttcacgtgagaaattcacatatgcggctgttttggaaggctcagtaccatgaagattatcatgcattgccataaaatttgcaatttttttgactgagtcatgacgtgtcaggagtacattgatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTACCTGGGGAATCCAAGGTCATCCTAGTTGCATACGCAAACAG
                                                                    |  | | |    |  |||||   ||    |   ||    ||  | |  ||||||    | ||| | ||   ||||| |  |             |    |||  |   ||  ||||||| | ||||||||||||||||| |||||||||||  | |||||||| || ||||  ||  |||| || ||    ||   |   || |||
-----------------------------------------------------------------gggcggacaggaattttatttggtttgcgtgttgatattgtcatcctta--cattgc----atattgggaaaccttttggcaaa------------taaacttactatatggttacagGTGGATATATCATCATTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
















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|208362728|gb|DC947191.1|DC947191
EST:     GCACTGC-GGNAAATA-TTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTANTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|208395643|gb|DC924193.1|DC924193
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|208387294|gb|DC933045.1|DC933045
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|208380398|gb|DC907723.1|DC907723
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACNATG                         GTGGGTGTATCATCATTATNGTGCGATGGTGATGNCATNANTGAGTCTNAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|208379652|gb|DC903707.1|DC903707
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATNGTGCGATGGTGATGNCATTAGTGAGTCT
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCT
EST: gi|208371674|gb|DC932503.1|DC932503
EST:     NCACTGCGGGAAAATATTTTGANAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATNGTGCNATGGTGATGGCA
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCA
EST: gi|208351804|gb|DC910358.1|DC910358
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTANTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|208363415|gb|DC947013.1|DC947013
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
EST: gi|100445691|gb|CJ969990.1|CJ969990
EST:     GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATG                         GTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC
genomic: GCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 24

GCTTGGTTATTGTTTTTCTACACTAGTTTAGCACTGCGGGAAAATATTTTGAGAGTCAACGGTAGTGACATACGACCATGgtactttcat ... gatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTACCTGGGGAATCCAAGGTCATCCTAGTTGCATACGCAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcaatttttttgactgagtcatgacgtgtcaggagtacattgatgtggcagGTGGGTGTATCATCATTATTGTGCGATGGTGATGGCATTAGTGAGTCTTACCTGGGGAATCCAAGGTCATCCTAGTTGCATACGCAAACAG
      aatttttttga  TA-rich tract