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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccctcaacttcaacaaactagcagatttgtgtcttttaatctgttgcaagcaaattccagttcttgtttatttattcatttatttattttttcgttaagcaatcaaggcaactgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTATTAAGGGCTTTGGTCGTGGCTCAAAATTGCTTGGGACTCCCACTG

Basic information

species Physcomitrella patens
transcript PP1S79_94V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_94V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv00s0181g00140.t01 (Vitis vinifera), 3'ss of exon 7
gtaactccctcaacttcaacaaactagcagatttgtgtcttttaatctgttgcaagcaaattccagttcttgtttatttattcatttatttattttttcgttaagcaatcaaggcaactgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTATTAAGGGCTTTGGTCGTGGCTCAAAATTGCTTGGGACTCCCACTG
                    || ||  |||||     |||| | || |  | ||| ||  | | |||     | | ||  |    ||| |||||||     | | | ||  |         ||||||  | |  |   |  ||||  ||||||| ||||| || |||||||| || |||||||| ||||||||||| |||||  | |||||    || || |
-----------------gtaaacctctcagat--acttcttatcatattct-caaacatttcctagtaaggttctcttggta---ttacttattttcat-ctgaactattgatttg-taactgcagGGGTCGAGGATACCTTACCAGTAGAGCCTTGGTATATAGGTGGGCCTGTCATTAAGGGATTTGGTCGTGGGTCAAAGGTACTTGGAGTCCCAACAG
















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|208359039|gb|DC957787.1|DC957787
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATC                         GAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
EST: gi|67696608|gb|BJ956841.1|BJ956841
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATC                         GAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
EST: gi|162214903|gb|FC390463.1|FC390463
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATC                         GAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
EST: gi|100356058|gb|BY946175.1|BY946175
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATC                         GAATTGGTGGCGCTATACCTATAGAGCCATGGTAC
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTAC
EST: gi|208360015|gb|DC939319.1|DC939319
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAA-TGATC                         GAATTGGTGGCGCTATACCTATAGAGC-ATGGTACATGGGTGGGCCAGTTA
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTA
EST: gi|208360201|gb|DC939198.1|DC939198
EST:     TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATC                         NAATTGGTGGCGCTATACCTATAGAGC
genomic: TCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGC

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: 34 (upstream exon), 25 (downstream exon)
Score: 5

TCCAAGGATGCCCGTCCACAATACTCTTCAGCTGACGTAATATATTCTTCTCTGTTGGATTTTCAGCCTGAAGTCTGGGGCTTCCCCTCTCTAAATGATCgtaactccct ... actgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTATTAAGGGCTTTGGTCGTGGCTCAAAATTGCTTGGGACTCCCACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatttattcatttatttattttttcgttaagcaatcaaggcaactgttgcagGAATTGGTGGCGCTATACCTATAGAGCCATGGTACATGGGTGGGCCAGTTATTAAGGGCTTTGGTCGTGGCTCAAAATTGCTTGGGACTCCCACTG
     tttattcatttattta  TA-rich tract