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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccgctacacttgttgggtctgatttgaagatactagacctgatttaaccttgcttgaactcttgaatttagagttgttcgagaaaattggcatgcgattatctgaataagaaactaacttggctcaatattcaccacgccttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGCCTGGACCTGTGTTTCAACATCGCTGGCGTGTCGAATCCTAGTGTTCCAG

Basic information

species Physcomitrella patens
transcript PP1S6_39V6.1
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|37827254|gb|BJ585266.1|BJ585266
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|18339765|gb|BJ171792.1|BJ171792
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|37827409|gb|BJ585421.1|BJ585421
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|18333386|gb|BJ165400.1|BJ165400
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|37831788|gb|BJ589800.1|BJ589800
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|208367373|gb|DC951291.1|DC951291
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|208396889|gb|DC924389.1|DC924389
EST:     GAACGACTATCACCATGCTCACTCTGCNTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTNGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|67727030|gb|BJ977289.1|BJ977289
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|67725248|gb|BJ975507.1|BJ975507
EST:     GGACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|208363254|gb|DC954398.1|DC954398
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|67725844|gb|BJ976103.1|BJ976103
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|208360245|gb|DC950218.1|DC950218
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|208397969|gb|DC916724.1|DC916724
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
EST: gi|37842274|gb|BJ600282.1|BJ600282
EST:     GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGG                         GCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC
genomic: GAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGC

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: 34 (upstream exon), 13 (downstream exon)
Score: 4

GTTTGCAATCGATCAGTCGACGGGACGTGGTGGAACTATCATCGATTCCGGAACGACTATCACCATGCTCACTCTGCCTGCATATAGTGCTGTCTTGAGGgtaacccgct ... ttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGCCTGGACCTGTGTTTCAACATCGCTGGCGTGTCGAATCCTAGTGTTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatctgaataagaaactaacttggctcaatattcaccacgccttatgtacagGCATACGAATCCTTTGTCAACTACCCTCGGTTGGATGGTTCCGCATACGGCCTGGACCTGTGTTTCAACATCGCTGGCGTGTCGAATCCTAGTGTTCCAG
                aactaac  putative branch site (score: 4)
         aataagaaa  TA-rich tract