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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaaagatttattatgtttcaatttttataatttttgacgtaaaatttatttgtggagaattcttttccaaaattttctctattgttctgatgcatctacttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACCGCTACTTTGACCCCAAAACTGTCGGCTTAGACTTCGATGGCATGATGGA

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.2
intron # 6
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|208372110|gb|DC940292.1|DC940292
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|67574849|gb|BJ947673.1|BJ947673
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGG
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGG
EST: gi|100359406|gb|BY984238.1|BY984238
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAAACACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|162217709|gb|FC393801.1|FC393801
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|100397833|gb|BY990424.1|BY990424
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|162172938|gb|FC348943.1|FC348943
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|208359935|gb|DC938956.1|DC938956
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|162167595|gb|FC343740.1|FC343740
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|100373109|gb|BY949215.1|BY949215
EST:     NCA-CGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGNN                         N
genomic: -CAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacag-
EST: gi|100373109|gb|BY949215.1|BY949215
EST:     NCA-CGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGNN                         N
genomic: -CAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacag-
EST: gi|162157447|gb|FC333211.1|FC333211
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|100361559|gb|BY984067.1|BY984067
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
EST: gi|208364270|gb|DC935541.1|DC935541
EST:     TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGG                         GAAACCACAANAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC
genomic: TCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACC

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: 25 (upstream exon), 30 (downstream exon)
Score: 7

GTCCAAGGCCTTTCTGGTACGGGTTCTCTTCGCTTGGGTGCTGCTTTCATTCAACGTTACTTCCCTGGCATCACCGTTTACATCTCTTCTCCAACTTGGGgtaagacaaa ... acttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACCGCTACTTTGACCCCAAAACTGTCGGCTTAGACTTCGATGGCATGATGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagaattcttttccaaaattttctctattgttctgatgcatctacttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACCGCTACTTTGACCCCAAAACTGTCGGCTTAGACTTCGATGGCATGATGGA
                                ttctgat  putative branch site (score: 7)
                                          tctacttc  putative PPT
                aaaattttctctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaaagatttattatgtttcaatttttataatttttgacgtaaaatttatttgtggagaattcttttccaaaattttctctattgttctgatgcatctacttcaacagGAAACCACAAGAACATATTTAATGATGCTGGTGTCCCATGGAAAGAATACCGCTACTTTGACCCCAAAACTGTCGGCTTAGACTTCGATGGCATGATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA