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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcatttatccctttgacccattaaatcgtgtttcctgtgtccacatgtctaatgttgtacttcgactgtgagtttagaaatttttgataacaaggaatcgcctatccttatgctaccttgcttcgtgtgtttgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACTGGAGCCGGTGATGCATTTTGTGCTGGTCTTCTGAGCCAGCTTGCGAAGT

Basic information

species Physcomitrella patens
transcript PP1S127_105V6.1
intron # 5
splice site 3'
intron type U2

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|67720181|gb|BJ970440.1|BJ970440
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162255602|gb|FC431600.1|FC431600
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162159123|gb|FC334294.1|FC334294
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|19783707|gb|BQ040057.1|BQ040057
EST:     GTGCACAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|18335485|gb|BJ167505.1|BJ167505
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|18340869|gb|BJ172900.1|BJ172900
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|18339396|gb|BJ171423.1|BJ171423
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|208396708|gb|DC920388.1|DC920388
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162193816|gb|FC371291.1|FC371291
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162255603|gb|FC431601.1|FC431601
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162159124|gb|FC334295.1|FC334295
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|67724820|gb|BJ975079.1|BJ975079
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162197072|gb|FC372450.1|FC372450
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162263645|gb|FC438881.1|FC438881
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162197071|gb|FC372449.1|FC372449
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|208386135|gb|DC949046.1|DC949046
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|6102385|gb|AW126855.1|AW126855
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTAAAGTGGTT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTT
EST: gi|162280370|gb|FC456075.1|FC456075
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162263646|gb|FC438882.1|FC438882
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162193789|gb|FC371290.1|FC371290
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
EST: gi|162280371|gb|FC456076.1|FC456076
EST:     GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT
genomic: GGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACT

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: 34 (upstream exon), 34 (downstream exon)
Score: 14

CGACCCCAAGGATGATGCACACAACCTGAAAATGATGCCCGCTGGCTGCAGGTTGATGCTAGTGACGGAGGGTGCAGAAGGCTGTCGTTATTACACCCCGgtatttgcat ... tgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACTGGAGCCGGTGATGCATTTTGTGCTGGTCTTCTGAGCCAGCTTGCGAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacaaggaatcgcctatccttatgctaccttgcttcgtgtgtttgaaatacagAAATTTCATGGCCAAGTGGGAGGTCTCAAGGTTCAAGTGGTTGATACCACTGGAGCCGGTGATGCATTTTGTGCTGGTCTTCTGAGCCAGCTTGCGAAGT
 tgataac  putative branch site (score: 14)
                                           tttgaaata  TA-rich tract