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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgtccactgaagttgttttggaagcataccccatgcgtagtttctgggaatgtcattatataccttgcagcattcatggaccaacatgcactagagctgtgttctgcattttgttcattattaacgtgatgatttgtattcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGAGACGGCTTGCAGAATGAGAAGACGACTGTCCCTACCCACGTGAAAGTGA

Basic information

species Physcomitrella patens
transcript PP1S138_43V6.1
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|208389033|gb|DC937366.1|DC937366
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGAA-ATTGTGGAAGTGGG
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGG
EST: gi|208397502|gb|DC908322.1|DC908322
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGAA-ATTGTGGAANTGGGG
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGG
EST: gi|208353132|gb|DC913890.1|DC913890
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACC-AAG                         CTACTGANAGGATTGCC-AGTTATGTGAA
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAA
EST: gi|100385660|gb|BY987725.1|BY987725
EST:     GCGACTCCGACAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGCAGATTGTGGAAGTGCGGCCGCGA
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGA
EST: gi|208358936|gb|DC939220.1|DC939220
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCNAAG                         CTACTGAGAGGATTGCCCAGT
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGT
EST: gi|100429318|gb|BY978050.1|BY978050
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGA
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGA
EST: gi|100436724|gb|BY979494.1|BY979494
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCNAG                         CTACTGAGAGGATTGCCCAGT
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGT
EST: gi|162207542|gb|FC383995.1|FC383995
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGA
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGA
EST: gi|208389798|gb|DC937433.1|DC937433
EST:     GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAG                         CTACTGAGAGGATTGCCCAGTTATGTGA-GATTGTGGAAG
genomic: GCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAG

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: 18 (upstream exon), 31 (downstream exon)
Score: 6

CAATGTGGTGAATGGCGAACGAGGCCTTTTGATGTCGTCGCAAGAAAATGGCGACTCCGAAAATGCGAACACGGATGGGATGAAGCGCTTCCGACCCAAGgtgaatgtcc ... attcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGAGACGGCTTGCAGAATGAGAAGACGACTGTCCCTACCCACGTGAAAGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagctgtgttctgcattttgttcattattaacgtgatgatttgtattcttgcagCTACTGAGAGGATTGCCCAGTTATGTGAAGATTGTGGAAGTGGGGCCGCGAGACGGCTTGCAGAATGAGAAGACGACTGTCCCTACCCACGTGAAAGTGA
                          tattaac  putative branch site (score: 6)
                                            tattctt  putative PPT
               attttgttcattatta  TA-rich tract