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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaagtttaaccacgccaactcgtttaggttaagaaatatttttggggttgttttgtttataacgtgtgtacacaactcatgaacttacttttgggggtctctaacatcgttggactatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG

Basic information

species Physcomitrella patens
transcript PP1S197_12V6.1
intron # 3
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|37853644|gb|BJ611652.1|BJ611652
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|67691341|gb|BJ951574.1|BJ951574
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|208399259|gb|DC912460.1|DC912460
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|37833887|gb|BJ591899.1|BJ591899
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|162199893|gb|FC376459.1|FC376459
EST:     ATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|67717109|gb|BJ967368.1|BJ967368
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|37841975|gb|BJ599983.1|BJ599983
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|162251127|gb|FC426404.1|FC426404
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|67508124|gb|BJ940995.1|BJ940995
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|162251128|gb|FC426405.1|FC426405
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|18352449|gb|BJ184503.1|BJ184503
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|37848516|gb|BJ606524.1|BJ606524
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|208350547|gb|DC926238.1|DC926238
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|18360281|gb|BJ192343.1|BJ192343
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|18367956|gb|BJ200040.1|BJ200040
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|67725632|gb|BJ975891.1|BJ975891
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
EST: gi|18364782|gb|BJ196855.1|BJ196855
EST:     ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAG                         TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA
genomic: ACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGA

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), 34 (downstream exon)
Score: 36

ACGGCGCTGAAGTTCGAACCGACAAACCTCGGAAAACCACAAAGTACATGACCAAATATGAACGAGCTAGAGTGCTTGGTACTCGTGCTCTTCAAATCAGgttagaagtt ... tatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaactcatgaacttacttttgggggtctctaacatcgttggactatcttacagTATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG
                            ctctaac  putative branch site (score: 36)
                                            ctatctt  putative PPT
              ttactttt  TA-rich tract