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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctttctgcgaaccatctgtgcctcgtgccgttttacttcttgctctatttttgtttgtagacaccaagatagaatatcatgcttattgtttgaatttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAGAGGGCTTTCCGTGATGCTTACAAAAGTTTCCCGAGCGGCCACGTCTCAT

Basic information

species Physcomitrella patens
transcript PP1S4_56V6.1
intron # 4
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|162274342|gb|FC450310.1|FC450310
EST:     GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCG                         GAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG
genomic: GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCGgtatggcttt ... tttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG
EST: gi|162268064|gb|FC443534.1|FC443534
EST:     GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCG                         GAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG
genomic: GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCGgtatggcttt ... tttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG
EST: gi|162278048|gb|FC453867.1|FC453867
EST:     GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCG                         GAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG
genomic: GAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCGgtatggcttt ... tttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAG

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: 15

TGCCATCGTGATCACAGCCCTCTTCACAGATTCTATCAAGAATCTGGTTGGAATGCCGCGCCCGGACTTTTTCCACCGGTGCTTTCCTGATGGTAAAGCGgtatggcttt ... tttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAGAGGGCTTTCCGTGATGCTTACAAAAGTTTCCCGAGCGGCCACGTCTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttgtagacaccaagatagaatatcatgcttattgtttgaatttccaacagGAATACACGGCTGATTTGGAGCGGCGAGTTATCTGCCATCCCGGCGACGAGAGGGCTTTCCGTGATGCTTACAAAAGTTTCCCGAGCGGCCACGTCTCAT
                                             tttcc  CT-rich tract
                                 ttattgtttgaattt  TA-rich tract