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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattggaagctgaaatgaagtatctctataaaaaaaactttcatttcgtactcagatagatgaaggttcatgtagcagttgatggcttataataa...

Basic information

species Physcomitrella patens
transcript PP1S91_247V6.1
intron # 4
splice site 5'
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|208349685|gb|DC917863.1|DC917863
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|37852656|gb|BJ610664.1|BJ610664
EST:     TGTTGTTGGAGGTCATGCAGGCATTACCATCCTTNCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: TGTTGTTGGAGGTCATGCAGGCATTACCATCCTT-CCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162209148|gb|FC385367.1|FC385367
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|37848128|gb|BJ606136.1|BJ606136
EST:     CTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTTCTTACCAA
genomic: CTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGC-TCTTACCAA
EST: gi|67726357|gb|BJ976616.1|BJ976616
EST:     CTGGTG-TGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|37844544|gb|BJ602552.1|BJ602552
EST:     GGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: GGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|100392213|gb|BY953250.1|BY953250
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAA
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAA
EST: gi|37821977|gb|BJ580043.1|BJ580043
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162181210|gb|FC357629.1|FC357629
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|208367832|gb|DC954905.1|DC954905
EST:     CTGTTG-TGGAGGTCATGCAGGCA-TACCATCCTTCCCCTG-TTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162214047|gb|FC389885.1|FC389885
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162178434|gb|FC354158.1|FC354158
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162181211|gb|FC357630.1|FC357630
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGT
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGT
EST: gi|162151333|gb|FC327462.1|FC327462
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|100402373|gb|BY954803.1|BY954803
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GGCACTCCCA-GGTTGATTTGAGTGACGAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAG
EST: gi|67694051|gb|BJ954284.1|BJ954284
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|100396841|gb|BY953854.1|BY953854
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAAGGT-GATTTGAGTGACGAGGAACTCGACGCTCTTACCAA
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAA-GGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAA
EST: gi|37850258|gb|BJ608266.1|BJ608266
EST:     TGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: TGTTGTTGGAGGTCATGCAGGCATTACCATCCTT-CCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|67693648|gb|BJ953881.1|BJ953881
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|208370637|gb|DC948230.1|DC948230
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162232670|gb|FC409221.1|FC409221
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|19784263|gb|BQ040147.1|BQ040147
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGNTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|37840408|gb|BJ598416.1|BJ598416
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162214048|gb|FC389886.1|FC389886
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTAC-AAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|67726305|gb|BJ976564.1|BJ976564
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
EST: gi|162151332|gb|FC327461.1|FC327461
EST:     CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG                         GCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG
genomic: CTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAG

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

ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattg ... tttggttcagGCCACTCCCAAGGTTGATTTGAGTGACGAGGAACTCGACGCTCTTACCAAGCGTACTCAAGATGGTGGAACGGAGGTCGTCCAAGCTAAGGCCGGCAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAGgtgactattggaagctgaaatgaagtatctctataaaaaaaactttcatttcgtactcagatagatgaaggttcatgtagcagttgatggcttataataa

- - - - - - - - - TTGGAG
- - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaaa