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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcag

Basic information

species Physcomitrella patens
transcript PP1S153_101V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA19G44090.1 (Glycine max), 5'ss of exon 7
AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactattgtt--tctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcag
 |||||||||| |||||||| |||||||||||||| |||||  |  | || || ||||| |  |||||  |  | |    |  |    | ||| ||||||      |  ||   || |  | |   ||||||     | | || | |     | |                   
CATAAGTGCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGGATCCGGAAGgtaaagctattaataatttatttgtctatcatggttttgatattg---gatcacaatgcatgatct--acgaagca----tgaactgggtttctgtattgcag--------------

upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA03G41500.1 (Glycine max), 5'ss of exon 6
AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactattgtt--tctcgcagagttctgttgttctgatatc--acctaagtacc-tggcttt----gtgtcggc-gaagctctgttcagctagatcctgatttaatgatt-cacttgtcgcag------------------------------------
 |||||||||| |||||||| |||||||||||||| |||||  |  | || || ||||| |   ||||  |  | |    |  ||   | ||| | ||||   |||  | |||| || | |     |  |   | |    |||||   ||    ||||| | |    |||       || |                                      
CATAAGTGCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGGATCCGGAAGgtaaagttattaatcatttatttgtctttcatggttttaatattggaccatattaccatgacctacgaagcatgaactgggtttctgtgttgcagattcctggtgtgccaattatgtacatcaccagacctacgaagcatgaactgggtttctgtgttgcag

upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA12G31740.1 (Glycine max), 5'ss of exon 8
AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactattgttt-ctcgcagagttctgttgttctgatatc--acctaagtacctggctttgtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcag
 | |||||||| |||||||| |||||||||||||| |||||  |  | ||||| ||||| |    ||| ||  ||     |  | || | ||   ||||   |||    | | || |    | |  | |    |||||    |                                
CACAAGTGCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatgacccattat--gtggttttctgtattacag------------------------------

upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA13G38690.2 (Glycine max), 5'ss of exon 8
AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactattgttt--ctcgcagagttctgttgttctgatatc--acctaagtacctggctttgtgtcggcgaagctctgtt-cagctagatcctgatttaatgattcacttgtcgcag
 | |||||||| |||||||| |||||||||||||| |||||  |  | ||||| ||||| |    ||| ||    |  |    ||   ||||| | ||||   |||    | || | |      || | |   || | || |||                                 
CACAAGTGCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcattattcacttttccatctttgattgttttaatattggaccctgatgccagacccatgatctgggtttctgtattacag---------------------------------

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|208359401|gb|DC939140.1|DC939140
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37822267|gb|BJ580333.1|BJ580333
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|100365650|gb|BY948205.1|BY948205
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208383700|gb|DC928031.1|DC928031
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37827579|gb|BJ585591.1|BJ585591
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208400155|gb|DC904803.1|DC904803
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|162206440|gb|FC383433.1|FC383433
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|162253618|gb|FC430356.1|FC430356
EST:     GTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208370447|gb|DC952150.1|DC952150
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208354670|gb|DC918696.1|DC918696
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37823705|gb|BJ581771.1|BJ581771
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG

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: 21 (upstream exon), 32 (downstream exon)
Score: 7

AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG




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