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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtatttttttgcactaacttctgaagctattctaactcaaggttcatagatgcaatgggtgaatgaatcagcctctcttcttggagcttgtgcgaagtcaaacacaggtggtcagtcttacatgttgcagaggcacaaaacccgcctcttttgacctagttgtttcgatttcgatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGAAGAATCTCGGAGTCATTGGTGTAGTATATGGCCTGATGGCGTTGGCAAC

Basic information

species Physcomitrella patens
transcript PP1S56_54V6.1
intron # 1
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|100366728|gb|BY985249.1|BY985249
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|208384909|gb|DC903416.1|DC903416
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|18332011|gb|BJ164023.1|BJ164023
EST:     TGATCGAAGACTGNGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|208400563|gb|DC904539.1|DC904539
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|18374616|gb|BJ206194.1|BJ206194
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|18349389|gb|BJ181438.1|BJ181438
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|208379795|gb|DC911680.1|DC911680
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
EST: gi|18361151|gb|BJ193216.1|BJ193216
EST:     TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAG                         ACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA
genomic: TGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGA

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: 27 (upstream exon), 20 (downstream exon)
Score: 5

ACGCATCCTCCACCAGAAACTAGCCAATCTCGGCGAGCATTTGATTCGTCTGATCGAAGACTGCGTTTGAATCGACCCCGATTTGCACCGTGAATTCTAGgtatggtatt ... gatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGAAGAATCTCGGAGTCATTGGTGTAGTATATGGCCTGATGGCGTTGGCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaggcacaaaacccgcctcttttgacctagttgtttcgatttcgatctagcagACATCCGTGACGTGAAGGTCACACTAGATCGCAGTTTTCTAATCGCAATGAAGAATCTCGGAGTCATTGGTGTAGTATATGGCCTGATGGCGTTGGCAAC
                     ttttgac  putative branch site (score: 5)