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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgttccgacttttcctaaatattgctccaccgactaatttaattttttattttgaactgctgtgatgtctgacattttagatttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGACGCGACAAGTTTGTCCATTAGATAACAGCGAATGGGAATTCCAGAAGTA

Basic information

species Physcomitrella patens
transcript PP1S123_104V6.1
intron # 2
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|18346564|gb|BJ178609.1|BJ178609
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCANCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67717972|gb|BJ968231.1|BJ968231
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37848549|gb|BJ606557.1|BJ606557
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18340374|gb|BJ172402.1|BJ172402
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67726475|gb|BJ976734.1|BJ976734
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18374779|gb|BJ206357.1|BJ206357
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGG-ATGGG                         GGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAG
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagG-TGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAG
EST: gi|162253473|gb|FC430107.1|FC430107
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGTAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18347997|gb|BJ180044.1|BJ180044
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|162256698|gb|FC433216.1|FC433216
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37822994|gb|BJ581060.1|BJ581060
EST:     CCAAGCGANCCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|162253474|gb|FC430108.1|FC430108
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGTAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37822761|gb|BJ580827.1|BJ580827
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37827369|gb|BJ585381.1|BJ585381
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37844984|gb|BJ602992.1|BJ602992
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67579222|gb|BJ951367.1|BJ951367
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67507928|gb|BJ940803.1|BJ940803
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18374414|gb|BJ205992.1|BJ205992
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18343562|gb|BJ175600.1|BJ175600
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37835442|gb|BJ593454.1|BJ593454
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67724913|gb|BJ975172.1|BJ975172
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|7047028|gb|AW476922.1|AW476922
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATGTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|37836148|gb|BJ594156.1|BJ594156
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|67716398|gb|BJ966658.1|BJ966658
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18353973|gb|BJ186028.1|BJ186028
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCA
EST: gi|37825672|gb|BJ583738.1|BJ583738
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
EST: gi|18343802|gb|BJ175840.1|BJ175840
EST:     CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGG                         GTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA
genomic: CCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGA

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: 76

GACAATTGTGCTATCTGCCGTAACCATATCATGGACTTGTGTATTGAGTGCCAAGCGAACCAAGCTAGTGCGACGAGTGAGGAGTGTACTGTGGCATGGGgtaagatgtt ... tttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGACGCGACAAGTTTGTCCATTAGATAACAGCGAATGGGAATTCCAGAAGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaattttttattttgaactgctgtgatgtctgacattttagatttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGACGCGACAAGTTTGTCCATTAGATAACAGCGAATGGGAATTCCAGAAGTA
     attttttattttgaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgttccgacttttcctaaatattgctccaccgactaatttaattttttattttgaactgctgtgatgtctgacattttagatttggttcagGTGTTTGCAATCACGCCTTCCATTTCCATTGCATCAGCAGATGGTTGAAGACGCGACAAGTTTGTCCATTAGATAACAGCGAATGGGAATTCCAGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT