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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgacttgttgacagcgcttgttgttcaaggtgttagggtttaggacgtgggaagggcagacgatgtgaaggttttgaggttggggttttagggtaaggtgttgtggaggtgcctgtgagcttgaattgtgaagtgttgttgcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCAGATGAGCGGACTCAGGTGCTCCAGGATATTGCTTCGGACCCTACGCTGC

Basic information

species Physcomitrella patens
transcript PP1S328_43V6.1
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|162269753|gb|FC444919.1|FC444919
EST:     ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAG                         GAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
genomic: ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
EST: gi|18349548|gb|BJ181598.1|BJ181598
EST:     ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAG                         GAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
genomic: ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
EST: gi|100442228|gb|BY981252.1|BY981252
EST:     ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAG                         GAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCG
genomic: ATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
EST: gi|37828507|gb|BJ586519.1|BJ586519
EST:     TGCCGAAATNGTGACCACCAG                         GAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
genomic: TGCCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
EST: gi|162235856|gb|FC412407.1|FC412407
EST:     CCGAAATTGTGACCACCAG                         GAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA
genomic: CCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCA

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: 31 (upstream exon), 24 (downstream exon)
Score: 14

TAACAATATTCTGTATCCGAGAGAGGATCGGGATAAGAAGGTTTTGCTCTACGCCTGCCGAAATTGTGACCACCAGgtgagttgac ... gcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCAGATGAGCGGACTCAGGTGCTCCAGGATATTGCTTCGGACCCTACGCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtgttgtggaggtgcctgtgagcttgaattgtgaagtgttgttgcttgagcagGAGGTTGCGGACAATAATTGCGTGTACAGAAATGAGGTGCTCCACAGTGCAGATGAGCGGACTCAGGTGCTCCAGGATATTGCTTCGGACCCTACGCTGC
                         ttgaatt  TA-rich tract