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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcttatttttgactggatgttgaaccactagtattacgtgtttttgttatacatttatttgtataataatttgttacagtttagctttttccttgatgccttaagatgacgtcattgttcagtgaatatacgtgttgacaagacattgcactttgtggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCT

Basic information

species Physcomitrella patens
transcript PP1S101_225V6.1
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|162152921|gb|FC329223.1|FC329223
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|162152920|gb|FC329222.1|FC329222
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTANAATACAAAACTGCATATTATTCATTTTATCTTCC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|100387744|gb|BY951744.1|BY951744
EST:     TCACCACTCCAGCAGGAGAAAGT-GATTTGTCGAANTATGTATAACCCAC                         TTATCTGCGAATCGTAAAATACAAAACTGCATATAAT-CATTTTATC
genomic: TCACCACTCCAGCAGGAGAA-GTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATC
EST: gi|100401204|gb|BY990883.1|BY990883
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTANAATACAAAACTGCATATAATTCATTTTATCTTCC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|100361028|gb|BY946877.1|BY946877
EST:     TCACCACTCCAGCAGGAGAAGTTTGATTTGT-GAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATACAAAACTGCATATAATTCATTTTATCTCCC
genomic: TCACCACTCCAGCAGGAGAAGTT-GATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|162230234|gb|FC406590.1|FC406590
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTANAATACAAAACTGCATATTATTCATTTTATCTTCC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|100383945|gb|BY987202.1|BY987202
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATACAAAAACTGCATATTATTCATTTTATCTTC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAA-CTGCATATTATTCATTTTATCTTC
EST: gi|100402689|gb|BY954960.1|BY954960
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATACAAAACTGCATATAATTCATTTTATCT-CC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|208345511|gb|DC909201.1|DC909201
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC
EST: gi|100396655|gb|BY990233.1|BY990233
EST:     ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCAC                         TTATCTGCGAATCGTAAAATANCAAA-CTGCATATNATTCATTTTTATCT-
genomic: ATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATA-CAAAACTGCATATTATTCATTTT-ATCTT

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), 32 (downstream exon)
Score: 9

GTCGAGTATCAGACAGCCTCTGGACAGATGTTGGACCTGATCACCACTCCAGCAGGAGAAGTTGATTTGTCGAAATATGTATTACCCACgtacgtatct ... tggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcattgttcagtgaatatacgtgttgacaagacattgcactttgtggattgcagTTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCT
                      tgttgac  putative branch site (score: 9)
            tgaatata  TA-rich tract