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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAAAGACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtgcattgcaaggttgatgctttttcttagatgtgctcatccatgggttggttgttttcaaggctttctcgactgcggttcaacttcaaaagtttcctttgctattgcctagaggcaagtatttacctcatttgtgactgcgatggtgcag

Basic information

species Physcomitrella patens
transcript PP1S61_296V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_296V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GRMZM2G157269_T01 (Zea mays), 5'ss of exon 15
GGATAAAGACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtgcattgcaaggttgatgctttttcttagatgtgctcatccatgggttggttgttttcaaggctttctcgactgcggttcaacttcaaaagtttcctttgctattgcctagaggcaagtatttacctcatttgtgactgcgatggtgcag
||||||||| || | | ||||| |||| ||| ||||||||||||| |||||||||||||           | |    ||||| | |  |  |  || |  | || |||| | |||||   |  || |  | |   | || || |    ||||    |||||||||  | |   |||                                       
GGATAAAGATGGCTACCACTGGCTGACTGGAAGAGTTGATGATGTTATCAATGTTAGgtaatcca---gctacttatttgattcatccttcttaattt--tgattcatgagatggtt---taaaaaggctgccaaaatgtgggt--gtttcatt--tttcctttgaaaat---tag---------------------------------------
















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|37821648|gb|BJ579714.1|BJ579714
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
EST: gi|37836534|gb|BJ594542.1|BJ594542
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
EST: gi|37825079|gb|BJ583145.1|BJ583145
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
EST: gi|67724644|gb|BJ974903.1|BJ974903
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
EST: gi|37834316|gb|BJ592328.1|BJ592328
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
EST: gi|67725835|gb|BJ976094.1|BJ976094
EST:     GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAG                         TGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC
genomic: GACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCC

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), 35 (downstream exon)
Score: 17

GGATAAAGACGGATTCTACTGGTTGACAGGACGAGTTGATGATGTGATCAATGTTAGgtgggttgtg ... gatggtgcagTGGACACCGCATAGGCACAGCCGAGGTTGAATCTGCGCTAGTATCGCATCCTCAGTGCGCTGAAGCTGCAGTCGTCGGGTTCGATCACGAG




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