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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgtgtgtcgtattatcatttgtacgaatgcctgctcctgtttgtcttactattggcattggcatttaagtttgatttttacttgagcgttcga...

Basic information

species Physcomitrella patens
transcript PP1S134_28V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S134_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 5'ss of exon 2
ACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgtgtgtcgtattatcatttgtacgaatgcctgctcctgtttgtcttactattggcattggcatttaagtttgatttttacttgagcgttcga
 ||  | |||||  |||||||||| |||||||| || || ||||||||||| ||||| || || || |||||||| || || ||||| ||||| || |||||| ||    | ||| |||  |   |  ||    | ||      || ||    ||||| |   |||   |||     |||  |                 
GCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcacagagtcttatggta--taatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcag-------------

upper sequence: PP1S134_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G40350.2 (Glycine max), 5'ss of exon 3
ACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgtg---tgtcgtattatcat-ttgtacgaatgcctgc--tcctgtttgtcttactat-tggc--attggcatttaagtttgatttttacttgagcgttcga--------------------------------------------
|||| | ||||| || ||||| |||||||||||||||||||||||||| |||||||||||  |||| |||||||||||||| ||||| |||||||| || |||||| | ||   | |     |||  | |  || |  | | ||   || |||    |  | ||| |||   |||||   |  ||| |  || | | ||  |    | |                                            
ACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCTATGCTATGGTTATAACTgtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtgatgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtttgtag

upper sequence: PP1S134_28V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G00330.1 (Glycine max), 5'ss of exon 3
ACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgtgtgtc--------gtattat-catttgtacgaatgcctgc--tcctgtttgtcttactat-tggc--attggcatt-------taagtttgatttttacttgagcgttcga--------------------------------------
|||| | ||||| || ||||| |||||||||||||||||||||||||| |||||||||||  |||| |||||||||||||| ||||| ||||| || || ||||||   | | |         |||||||    |||   |||    | |  || |||    |  | ||| |||   |||||   |       ||  | ||||||||  |      | | |                                      
ACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCTATGCTATGGTCATAACTgtaagttgttattttactcaagagtattatatgcttgcttgaagagtttcagtcttgtagaacacaatatatggtgaattggtgatgcagtactagttatgatttttgttaacaactccaatggctgtgtctcacaacttcttgtccatctgtttgtag

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|162271925|gb|FC448135.1|FC448135
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|208391689|gb|DC942279.1|DC942279
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|208363490|gb|DC939723.1|DC939723
EST:     TCAGGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|100445886|gb|CJ970185.1|CJ970185
EST:     TCATGCACCANCAACTCATTGAGATTCTTANTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCANCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|162271924|gb|FC448134.1|FC448134
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|208375482|gb|DC940508.1|DC940508
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTT
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTT
EST: gi|18333050|gb|BJ165064.1|BJ165064
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|208366173|gb|DC955274.1|DC955274
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
EST: gi|208393584|gb|DC953519.1|DC953519
EST:     TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACG                         AATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA
genomic: TCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATA

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), 34 (downstream exon)
Score: 11

ACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTTATGCGATGGTTATCACGgtaagtatgt ... ctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTTCTTACTGTAATTCTGC




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