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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcttctaacctggtacacaaaaccatgattaccctagaaactatctcgcagtgaggttgcgatcattttttaattttattacacctttgtagtcaaatcttgttagtgtggatgtaatacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTTCTTCTCTGGCTTTCTACTAGTACTTTAACGCTTTTTCTTGGCATTGAGG

Basic information

species Physcomitrella patens
transcript PP1S53_215V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S53_215V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA02G10590.2 (Glycine max), 3'ss of exon 11
gtatatcttctaacctggtacacaaaaccatgattaccctagaaactatctcgcagtgaggttgcg--atcattttttaattttattacacctttgtagtcaaatcttgttagtg-tggatgtaatacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTTCTTCTCTGGCTTTCTACTAGTACTTTAACGCTTTTTCTTGGCATTGAGG
                               |   |   |||||| | |||    ||   | |||   ||||||||  |   ||||      | |  | | |    |  ||  |  |    | |  |   | ||||| |||||||||||||| || ||||||||||| || || ||||| || |||||||| |||     |||||| |||  |||  | || ||||| |||||| 
-------------------------------gtccattgtagaaaatttct----gtttagctgctttatcattttggatggttatcttgtttgtcaactaagcattcattcttaattctcgcatgatttttcagGTAGATTATGATGAGGCCATTTTTTTGTGGCGTGTAGATAAGAAAGATTTTCTTCTTTGGACCATTACTAGCACTACAACATTGTTCCTTGGTATTGAGA

upper sequence: PP1S53_215V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 11
gtatatcttctaacctggtacacaaaaccatgattaccctagaaactatctcgcagtgaggttgcgatcattttttaattttattacacctttgtagtcaaatcttgttagtgtggatgtaatacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTTCTTCTCTGGCTTTCTACTAGTACTTTAACGCTTTTTCTTGGCATTGAGG-
                  |  | ||||      ||    |||   |||| ||    ||       | | || || |   || | |   | ||  |  | || |||| |   ||          |   | ||||| |||||||||||||| || ||||||||||| || || ||||| || |||||||| |||     |||||| |||  |||  | || ||||| ||||||  
---------------cattgtagaaaatttctgtt----tagctgctatatccttttgga----tggttatcttatttgttaactgagcattcattcttaattcttttgcttg----------atttttcaggTAGATTATGATGAGGCCATTTTTTTGTGGCGTGTAGATAAGAAAGATTTTCTTCTTTGGACCATTACTAGCACTACAACATTGTTCCTTGGTATTGAGAT
















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|162215718|gb|FC391732.1|FC391732
EST:     TGTGCACTGGCTGCTATTGTCATATCTGCTGTTGTTGGTCTG                         GTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTT
genomic: TGTGCACTGGCTGCTATTGTCATATCTGCTGTTGTTGGTCTGgtatatcttc ... tacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTT




















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: 11 (upstream exon), 25 (downstream exon)
Score: 1

TGTGCACTGGCTGCTATTGTCATATCTGCTGTTGTTGGTCTGgtatatcttc ... tacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTTCTTCTCTGGCTTTCTACTAGTACTTTAACGCTTTTTCTTGGCATTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttattacacctttgtagtcaaatcttgttagtgtggatgtaatacgctgcagGTTGATTATGATGAGGCAATATTTTTGTGGCGAGTGGACAAGAAGGACTTTCTTCTCTGGCTTTCTACTAGTACTTTAACGCTTTTTCTTGGCATTGAGG
 ttttaat  putative branch site (score: 1)
                                       atgtaata  TA-rich tract