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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaaaaattaatggtccttcacatactttctacattcagcataactttcttcgagtctcagttgataatgattcacgtcgtgatttgaacctggataggttggtgaaaatttgcggagtaattcctaacaaaatatctcctcaggggtacttaattctactacctattttgctttttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGGCCGTCTTTCATGGAGATTGCATATTCCGAAATGGAGGAAATTGAAAGAG

Basic information

species Physcomitrella patens
transcript PP1S83_49V6.3
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|67570112|gb|BJ942936.1|BJ942936
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|162219043|gb|FC394938.1|FC394938
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|67693377|gb|BJ953610.1|BJ953610
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|162241802|gb|FC418057.1|FC418057
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|7584271|gb|AW700167.1|AW700167
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|162241801|gb|FC418056.1|FC418056
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|162243976|gb|FC422318.1|FC422318
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
EST: gi|162246050|gb|FC424396.1|FC424396
EST:     CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAG                         TTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG
genomic: CGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGG

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), 33 (downstream exon)
Score: 11

AGAGCTACCCCTGGCCTTGGCATTGCCTTAGGTCTTTTTGGTGTTTTCCTCGTTGTGGATGGTATTTCATCGAGATTTTCTAAAAAGGATCATCATTGAGgtaacaaaaa ... tttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGGCCGTCTTTCATGGAGATTGCATATTCCGAAATGGAGGAAATTGAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatatctcctcaggggtacttaattctactacctattttgctttttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGGCCGTCTTTCATGGAGATTGCATATTCCGAAATGGAGGAAATTGAAAGAG
                   acttaat  putative branch site (score: 11)
                                 cctattttgctttttc  putative PPT
                  tacttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaaaaattaatggtccttcacatactttctacattcagcataactttcttcgagtctcagttgataatgattcacgtcgtgatttgaacctggataggttggtgaaaatttgcggagtaattcctaacaaaatatctcctcaggggtacttaattctactacctattttgctttttcgggcagTTGTGCGAGTTGCAGACGACTTGAAGCTGAAAAATTTGCAAACTTGGTTGGCCGTCTTTCATGGAGATTGCATATTCCGAAATGGAGGAAATTGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA