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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcttctattcagatttgtatcttgcagtgtggatgtctattgtgtgggtttcattccattggattgttcaatccgaagtcgtgattctctcaaggtcgttatcttgattagaattgtaatccttaatttcgtgttaatatttctttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGATGAGTCCAGCCTTACGGGAGAGCCCTTGGCTGTCCTGAAACAATCTGGG

Basic information

species Physcomitrella patens
transcript PP1S121_53V6.1
intron # 7
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|162234164|gb|FC410768.1|FC410768
EST:     TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGG                         GATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
genomic: TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
EST: gi|162256487|gb|FC432518.1|FC432518
EST:     TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGG                         GATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
genomic: TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
EST: gi|162196153|gb|FC373494.1|FC373494
EST:     TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGG                         GATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
genomic: TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
EST: gi|162154985|gb|FC331403.1|FC331403
EST:     TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGG                         GATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
genomic: TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
EST: gi|162179692|gb|FC355750.1|FC355750
EST:     TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGG                         GATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT
genomic: TTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGAT

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: 29 (upstream exon), 34 (downstream exon)
Score: 7

TCGCCTTGTCATGGGATTTGACAACAGTGGCCATCCAACTACTGTGACTGTTCCCTGCGATAGCTTATCTGTTGGAGACTCAGTTGTTGTGTTGCCTGGGgtatgctctt ... ttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGATGAGTCCAGCCTTACGGGAGAGCCCTTGGCTGTCCTGAAACAATCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttgattagaattgtaatccttaatttcgtgttaatatttctttcttgacagGATCGAATCCCTGTGGACGGTGTAGTCAAGTCCGGAAAGAGCACTGTGGATGAGTCCAGCCTTACGGGAGAGCCCTTGGCTGTCCTGAAACAATCTGGG
                                tgttaat  putative branch site (score: 7)
                                      tatttctttctt  CT-rich tract
                                  ttaatatttctttctt  TA-rich tract