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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcgtgtagatgaattgcttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAAGTGCTTCACAGGGATATCAAAG

Basic information

species Physcomitrella patens
transcript PP1S3_535V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_535V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ34303 (Selaginella moellendorffii), 3'ss of exon 3
gtacttcgtgtagatgaattgcttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAAGTGCTTCACAGGGATATCAAAG
                                                                                             |   |  | |    |    |   | |    |       ||| | |||  | |    |||||||||||||||||||||||||||| || ||  | ||||| ||| | |||||||| |||||  ||||||||||||
--------------------------------------------------------------------------------------------gtagagtttcacagctgcggtgctcccgggttctcaacataacacggtgcttt----tgcagTGTTATATGAAGCAGCTTCTCACCGGCCTTTACTACTGTCATATCAACCAAGTTCTTCATCGGGATATCAAAG

upper sequence: PP1S3_535V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ31297 (Selaginella moellendorffii), 3'ss of exon 4
gtacttcgtgtagatgaattgcttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAAGTGCTTCACAGGGATATCAAAG
                                                                                             |   |  | |    |    |   |||    |        || | |||  | |    |||||||||||||||||||||||||||| || ||  | ||||| ||| | |||||||| |||||  ||||||||||||
--------------------------------------------------------------------------------------------gtagagtttcacagctgcgatgctctcgggttctcaacacaacacggtgcttt----tgcagTGTTATATGAAGCAGCTTCTCACCGGCCTTTACTACTGTCATATCAACCAAGTTCTTCATCGGGATATCAAAG
















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|162186337|gb|FC361645.1|FC361645
EST:     CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAG                         TGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA
genomic: CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtg ... tataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA
EST: gi|67718151|gb|BJ968410.1|BJ968410
EST:     CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAG                         TGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA
genomic: CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtg ... tataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA
EST: gi|162156181|gb|FC332556.1|FC332556
EST:     CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAG                         TGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA
genomic: CTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtg ... tataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcagTGTTATATGAAGCAGCTTCTCACAGGTCTACATTACTGCCATGTGAACCAAGTGCTTCACAGGGATATCAAAG
                             gtttaat  putative branch site (score: 4)
                                        tcttctat  putative PPT
      attttttt  TA-rich tract