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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgttctgaaaaaccgcttcaccttattgtctatgtgctcatctaatttacgaaaatttgttgcgcactgtccgtcccttgttttgtagcacttgtcattgatttcggtgattgcaacgagtttcttactacacttttcatactgtgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCAATGGTTGTGAAAGCGTTTCCTGGAAAAGGCCAAAAACATCACACTAAAC

Basic information

species Physcomitrella patens
transcript PP1S41_314V6.1
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|100400448|gb|BY954482.1|BY954482
EST:     GG-CGACCATGAACATGGGCTCGGTGAATTAGTGCCCTTCTCTAAACA-G                         TTGTACGACAGTTCTTTGCAAGTGAGA
genomic: GGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAA-CAAGgtgtgtgttc ... tgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGA
EST: gi|208400797|gb|DC925077.1|DC925077
EST:     GGGCGACCATNNACATGGGCTCGGTGATTTAGTGCCCTTTCTCTAACAAG                         TTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCA
genomic: GGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCC-TTCTCTAACAAGgtgtgtgttc ... tgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCA
EST: gi|100387159|gb|BY951558.1|BY951558
EST:     CGGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAACAAG                         TTGTACGACAGTTCTTTGCCAGTGAGATTGGGGGGTACTGCGGGTATGGCA
genomic: CGGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAACAAGgtgtgtgttc ... tgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCA
EST: gi|67693160|gb|BJ953393.1|BJ953393
EST:     CGGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAACAAG                         TTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCA
genomic: CGGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAACAAGgtgtgtgttc ... tgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCA

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: 18 (upstream exon), 18 (downstream exon)
Score: 1

ACAGGAGAATGGGCTGCTTGGTGGCCTGCAAAACATGTGGAGCACACTGTCGGGCGACCATGAACATGGGCTCGGTGATTTAGTGCCCTTCTCTAACAAGgtgtgtgttc ... tgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCAATGGTTGTGAAAGCGTTTCCTGGAAAAGGCCAAAAACATCACACTAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcggtgattgcaacgagtttcttactacacttttcatactgtgcggcacagTTGTACGACAGTTCTTTGCAAGTGAGATTGGGGGTTACTGCGGGTATGGCAATGGTTGTGAAAGCGTTTCCTGGAAAAGGCCAAAAACATCACACTAAAC
                      ttcttac  putative branch site (score: 1)
                                  ttttcata  TA-rich tract