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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcttgaaaactctttatcatttttaccagtgattagtcctgtgtaaaatggaactcgttaatcttgcgctgattctcatttaacatattgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCAATGTGCGTTGATATCACAGACAACGAGCTGGCCTATCTTGAAAGCATTC

Basic information

species Physcomitrella patens
transcript PP1S250_15V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S250_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 3
aagcttgaaaactctttatcatttttaccagtgattagtc-ctgtgtaaaatggaactcgttaatcttgcgctga-ttctcatttaacatattgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCAATGTGCGTTGATATCACAGACAACGAGCTGGCCTATCTTGAAAGCATTC
                                  || ||| || ||           |  ||    || | | || || |  |||    | |  |    ||||| || ||||||||||| || |||||||| || || || || ||||| |||||||| || |||||||| || |||||||||||||| || || ||||| |
---------------------------------gttggtctctttggtttgcttcttttctttggtttacacggagtttttgtttgttctctctt---ccagTTTCGCACACACAAGGTGATCTATCGACGCTACGCCGGGCTCTTCTTCTCAATGTGTGTGGATATCACGGATAACGAGCTGGCCTACCTCGAGAGCATCC

upper sequence: PP1S250_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 3
aagcttgaaaactctttatcatttttaccagtgattagtc-ctgtgtaaaatggaactcgttaatcttgcgctga-ttctcatttaacatattgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCAATGTGCGTTGATATCACAGACAACGAGCTGGCCTATCTTGAAAGCATTC
                                  || ||| || ||           |  ||    || | | || || |  |||    | |  |    ||||| || ||||||||||| || |||||||| || || || || ||||| |||||||| || |||||||| || |||||||||||||| || || |||||  
---------------------------------gttggtctctttggtttgcttcttttctttggtttacacggaatttttgtttgttctctctt---ccagTTTCGCACACACAAGGTGATCTATCGACGCTACGCCGGGCTCTTCTTCTCAATGTGTGTGGATATCACGGATAACGAGCTGGCCTACCTCGAGAGCATCT
















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|208398466|gb|DC916493.1|DC916493
EST:     TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAG                         TTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
genomic: TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
EST: gi|208378131|gb|DC902604.1|DC902604
EST:     TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAG                         TTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
genomic: TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
EST: gi|208387424|gb|DC949209.1|DC949209
EST:     ATCCGNAGTTCACTAATTTCGTAGAG                         TTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
genomic: ATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
EST: gi|100428997|gb|BY977888.1|BY977888
EST:     TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAGTTTCGTAGAG                         TTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
genomic: TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
EST: gi|208361368|gb|DC935083.1|DC935083
EST:     TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAG                         TTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA
genomic: TTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCA

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: 12 (upstream exon), 31 (downstream exon)
Score: 2

GTTCATAGGCTGGTTGTTAATAGGGATCCGAAGTTCACTAATTTCGTAGAGgtaagtgtct ... tgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCAATGTGCGTTGATATCACAGACAACGAGCTGGCCTATCTTGAAAGCATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatggaactcgttaatcttgcgctgattctcatttaacatattgtggaacagTTCCGAACACACAAGGTCATTTATCGACGTTATGCTGGCCTTTTCTTTTCAATGTGCGTTGATATCACAGACAACGAGCTGGCCTATCTTGAAAGCATTC
                                  atttaac  putative branch site (score: 2)
                                tcatttaacatatt  TA-rich tract