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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccactatttttatctgaacttcattacaagggctgaggttattgacttgtttccgtttcagcgttcacaatacctagtttcgtttgctgtaatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCATGTGCTTTGTGAAGGACCCATTACAGGTCGTGCAGCAGACGTCCTGGCT

Basic information

species Physcomitrella patens
transcript PP1S119_137V6.1
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|67569798|gb|BJ942622.1|BJ942622
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|208397136|gb|DC908150.1|DC908150
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100439250|gb|BY980169.1|BY980169
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGAATG-ATTCGTAGCTGTTGTTGCACATACCC
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGA-TGGATTCGTAGCTGTTGTTGCACATACCC
EST: gi|100384797|gb|BY950787.1|BY950787
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|162183958|gb|FC359328.1|FC359328
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100445208|gb|BY982837.1|BY982837
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|67719527|gb|BJ969786.1|BJ969786
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|162161202|gb|FC337265.1|FC337265
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100397823|gb|BY990419.1|BY990419
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|67716276|gb|BJ966536.1|BJ966536
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA

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: 33 (upstream exon), 29 (downstream exon)
Score: 15

TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCATGTGCTTTGTGAAGGACCCATTACAGGTCGTGCAGCAGACGTCCTGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtttccgtttcagcgttcacaatacctagtttcgtttgctgtaatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCATGTGCTTTGTGAAGGACCCATTACAGGTCGTGCAGCAGACGTCCTGGCT
 tattgac  putative branch site (score: 15)