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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttggacctgcattttgacatgccactgtctaatgtggatggttccctacatcaagcaggatggtattgattgtttctttttggtgggctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTCATCACGACATTGCTAATGACATACCAGCACATACTCAGCAACTACAGTA

Basic information

species Physcomitrella patens
transcript PP1S50_114V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S50_114V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
---aatttggacctgcattttgacatgccactgtctaatgtggatggttccctacatcaagcaggatggtattgattgtttctttttggtgggctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTCATCACGACATTGCTAATGACATACCAGCACATACTCAGCAACTACAGTA
   ||||  |  ||   || |  | |    |    |  ||  |    ||  |    |    | |  |  || | ||  |  | ||||      | || | ||||||||||| ||||||| || || ||||||||||| ||| | || ||| ||||||| |||||| | || || ||||||   ||    ||     | |||||
actaattaag--ctaatttgttgcttattgcc-catgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA

upper sequence: PP1S50_114V6.4 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
aatttggacctgcattttgacatgccactgtct-aatgtggatggttccctacatcaagcaggatggtat-tgattgtttctttttggtgggctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTCATCACGACATTGCTAATGACATACCAGCACATACTCAGCAACTACAGTA
  ||||   |||   |||        | ||  | |||  || ||  |       ||| ||||  |   || | | | |   | |||      |||||| ||||||| ||| |||| ||||| |||||||||||||| ||| | ||  || ||||||| |||||||| ||||| ||||||   |||   ||| |  | |||||
-gtttg--tctgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattcttt------ctttgg-cagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA
















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|67695428|gb|BJ955661.1|BJ955661
EST:     AGCTGCAGC-AAAG                         C-NGTANTCTCA-TGAGGAC-AAAANTGGCCACCG-TTGTTCCAA-TCTTC
genomic: AGCTGCAGCAAAAGgttggtagtg ... ctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctacatcaagcaggatggtattgattgtttctttttggtgggctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTCATCACGACATTGCTAATGACATACCAGCACATACTCAGCAACTACAGTA
                     tattgat  putative branch site (score: 3)
                              tttcttttt  TA-rich tract