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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcctctttcgaatgttagttgcaacgtctatgctgctctgcttctatagcctgagtctaggatatgtagatatgtatggcgcaagaatcaatgaaagtagatatacccgcacctgactgattcttgtgaatctagaaagcttagtcaccttacgaaagcaagtgtggtttgtatag

Basic information

species Physcomitrella patens
transcript PP1S49_256V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 8
GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcctctttcgaatgttagttgcaacgtctatgctgctctgcttctatagcctgagtctaggatatgtagatatgtatggcgcaagaatcaatgaaagtagatatacccgcacctgactgattcttgtgaatctagaaagcttagtcaccttacgaaagcaagtgtggtttgtatag
| |||||||| ||||||||  | || ||||| ||||| || || || || ||||| |||||||| ||||| || || ||||| |||||||||||||||||||    || ||  || |  | |||           |||| || | | |   | |||         ||  |   || | ||||     |  | | |||| |||||||  |  |  |                                                                    
GCGGTGATAATGAGGTTCAGCGCACTATGCTTGAAATTGTGAATCAGCTTGATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgt----tttctgatttggctatta-----------tatgatgattttcactt-tagttcatactcagttttactacagatgttcactgtta-agtcaa-gaaagtatctccaagcatg-----------------------------------------------------------------

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 8
GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcctctttcgaatgttagttgcaacgtctatgctgctctgcttctatagcctgagtctaggatatgt-agatatgtatggcgcaagaatcaatgaaagtagatatacccgcacctgactgattcttgtgaatctagaaagcttagtcaccttacgaaagcaagtgtggtttgtatag
| |||||||| ||||||||  | || ||||| ||||| || || || || ||||| |||||||| ||||| || || ||||| |||||||||||||||||||    || ||  || |  | |||  |   |  |  |   |  |        |        |   | | || || |   | ||||  | |   | |  || || ||                                                                              
GTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAATTGTGAATCAGCTTGATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgt----tttctgatttggctatta--tatgattttcactttagttcatactcagttttactgcagatgttaagtcaagaaagtatctcactttagttcatcaa-gtg-----------------------------------------------------------------------------

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 8
GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcctctttcgaatgttagttgcaacgtctatgctgctctgcttcta-tagcctgagtctaggatatgtagatatgtatggcgcaagaatcaatgaaagtagatatacccgcacctgactgattcttgtgaatctagaaagcttagtcaccttacgaaagcaagtgtggtttgtatag
| || || ||||| || ||||| || |||||||| || ||||| || || |||||||||||||| ||||| || |||||||| |||||||| || ||||||||         |     | ||   || |||  || |   | |  | || | |  ||                                                                                                                               
GTGGCGACAACGAAGTGCAAAGGACGATGCTCGAGATTGTCAATCAGCTTGATGGTTTTGATGCTCGTGGGAACATTAAAGTTTTGATGGCCACGAACAGgtactgccgacttcatctaagtcttttccaa--tcaaacttacattactccaaacag-------------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 8
GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcctctttcgaatgttagttgcaacgtctatgctgctctgcttcta-tagcctgagtctaggatatgtagatatgtatggcgcaagaatcaatgaaagtagatatacccgcacctgactgattcttgtgaatctagaaagcttagtcaccttacgaaagcaagtgtggtttgtatag
| || || ||||| || ||||| || |||||||| || ||||| || ||||||||||||||||| ||||| || |||||||| |||||||| || ||||||||         |     | ||   || |||  || |   | |  | || | |  ||                                                                                                                               
GTGGCGACAACGAAGTGCAAAGGACGATGCTCGAGATTGTCAATCAGCTGGATGGTTTTGATGCTCGTGGGAACATTAAAGTTTTGATGGCCACGAACAGgtactgccgacttcatctaagtcttttccaa--tcaaacttacattactccaaacag-------------------------------------------------------------------------------------------------------------------------------

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|208386966|gb|DC956935.1|DC956935
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67720356|gb|BJ970615.1|BJ970615
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67727435|gb|BJ977694.1|BJ977694
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|37834307|gb|BJ592319.1|BJ592319
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|208361197|gb|DC954303.1|DC954303
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67725511|gb|BJ975770.1|BJ975770
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67578758|gb|BJ950925.1|BJ950925
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67726155|gb|BJ976414.1|BJ976414
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|208380596|gb|DC919368.1|DC919368
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|37839264|gb|BJ597272.1|BJ597272
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|37832375|gb|BJ590387.1|BJ590387
EST:     GATGGTTNTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACGTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|67700123|gb|BJ960356.1|BJ960356
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
EST: gi|208400821|gb|DC925101.1|DC925101
EST:     GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAG                         ACCAGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA
genomic: GATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAA

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: 35 (upstream exon), 35 (downstream exon)
Score: 29

GAGGTGATAACGAGGTTCAAAGAACAATGCTCGAAATAGTCAACCAACTGGATGGTTTTGATGCCCGTGGTAATATTAAAGTATTGATGGCAACTAACAGgtaagattcc ... gtttgtatagACCTGATACTCTGGATCCAGCGCTTTTACGGCCAGGTCGGTTAGATCGTAAGGTGGAGTTCGGGTTGCCTGATCTTGAAAGTCGAACCCAAATTTTCAAG




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