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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcgggatctttagggaatatggagtatagtttattgattctggtatacagtgcttttgctaggattagattctaatagtattagcagttgggtttcagGTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTTGGATTACCCCGGGAGCATGAGTTTTGGAGCAGAGGCATCAGTGCGTGTG

Basic information

species Physcomitrella patens
transcript PP1S9_92V6.1
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|162158252|gb|FC335295.1|FC335295
EST:     ATGTGGATGTCCGAAATCGACCTTTCACAGTCCGAAGTAGTGATAGTGAG                         GTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTT
genomic: ATGTGGATGTCCGAAATCGACCTTTCACAGTCCGAAGTAGTGATAGTGAGgtacttttta ... tgggtttcagGTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTT
EST: gi|162167745|gb|FC344059.1|FC344059
EST:     CACAGTCCGAAGTAGTGATAGTGAG                         GTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTT
genomic: CACAGTCCGAAGTAGTGATAGTGAGgtacttttta ... tgggtttcagGTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTT
EST: gi|100394968|gb|BY990013.1|BY990013
EST:     ATGTGGATGTCCGAAATCGACCTTTCACAGTCCGAAGTAGTGATAGTGAG                         GTAAAGTGTCACAGCAT
genomic: ATGTGGATGTCCGAAATCGACCTTTCACAGTCCGAAGTAGTGATAGTGAGgtacttttta ... tgggtttcagGTAAAGTGTCACAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacagtgcttttgctaggattagattctaatagtattagcagttgggtttcagGTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTTGGATTACCCCGGGAGCATGAGTTTTGGAGCAGAGGCATCAGTGCGTGTG
                          ttctaat  putative branch site (score: 2)
                         attctaatagtatta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgggatctttagggaatatggagtatagtttattgattctggtatacagtgcttttgctaggattagattctaatagtattagcagttgggtttcagGTAAAGTGTCACAGCATAATTATTGCGACGGGTGCTACAGCTAAGCGACTTGGATTACCCCGGGAGCATGAGTTTTGGAGCAGAGGCATCAGTGCGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG