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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggctattttgttggcggtgaatcgtcctttatcccacgttgatgatttttgcgggtgttcgcgtttacatgcaatcgctaatactatttgctgtgtgacttttgctaattgggaatgattttaacctggtcattcttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGCGAGACTAAG

Basic information

species Physcomitrella patens
transcript PP1S114_207V6.1
intron # 2
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|162173126|gb|FC348699.1|FC348699
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|162159953|gb|FC336206.1|FC336206
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|208393602|gb|DC904318.1|DC904318
EST:     ACGTCTCTCCGCAGGAGAATTACNTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAAGATCGTATGGCTCG
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCG
EST: gi|162159109|gb|FC334280.1|FC334280
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGNTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|162170578|gb|FC347074.1|FC347074
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|100376965|gb|BY949552.1|BY949552
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|67568739|gb|BJ941563.1|BJ941563
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
EST: gi|162197171|gb|FC374161.1|FC374161
EST:     ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAG                         TGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC
genomic: ACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGC

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), 32 (downstream exon)
Score: 13

GCACACTGGCAGTGACGACCACTGTGTACCCGATAGTGTCAAAGAATCGGACGTCTCTCCGCAGGAGAATTACTTCCTCGATGAATTGCTCCTCGCACAGgtggggctat ... ttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGCGAGACTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtgacttttgctaattgggaatgattttaacctggtcattcttttgaacagTGGGAGGATCGTATGGCTCGTGGACTTTTCCGTTATGACGTGACAGCCTGCGAGACTAAG
                            ttttaac  putative branch site (score: 13)
                                       tcattctttt  putative PPT
                       aatgattttaa  TA-rich tract