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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcagggtgttggagaacgtcaagattctccctgactttgaagctaatttgactcattgaggaatacatgtagtgtttagatgatgtgaacgaaccaaaagaggtctgaattgcggcagtaggttggtgtagaatcctgaatttcagttctatatgaactgacgttgcgtagctttgacgtttatgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCTGAGGCTATTGTAGGGGATGATCCCAATTTTCAAGGGCGGGGAAATCCTA

Basic information

species Physcomitrella patens
transcript PP1S342_20V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 5
gtaatgcagggtgttggagaacgtcaagattctccctgactttgaagctaatttgactcattgaggaatacatgtagtgtttagatgatgtgaacgaaccaaaagaggtctgaattgcggcagtaggtt--ggtgtagaatcctgaatttcagttctatatgaactgacgttgcgtagctt--tgacgtttatgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCTGAGGCTATTGTAGGGGATGATCCCAATTTTCAAGGGCGGGGAAATCCTA
                                                                                                   || | ||      | ||| |||| |   ||     | | | | |  |||     | | || |||   |  |||    |  ||    || || |       |||||||| ||||| || |||||||| || || |||||||| || ||||||||||| || |||||| | |||||||| |||||||| ||||| || |||||| 
---------------------------------------------------------------------------------------------------catatgaaactccagttggggcaatcttttcaaaggcacagttcataatgc--atgccat-tgagtggctgttatagaaattaacaactttcacttgtttcagAGTCCAAATGGTGTTTGGAACATTTTTGGTGGCAAGCTTGCATGGGGACCTGAAGCCATTGTATGTGATGATCCAAATTTTCAGGGGCGCGGGAATCCTT

upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 7
gtaatgcagggtgttggagaacgtcaagattctccctgactttgaagctaatttgactcattgaggaatacatgtagtgtttagatgatgtgaacgaaccaaaagaggtctgaattgcggcagtaggttg-gtgtagaat-cctgaatttcagttc-tatatgaactgacgttgcgtagctttgacgtttatgatcacc--agAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCTGAGGCTATTGTAGGGGATGATCCCAATTTTCAAGGGCGGGGAAATCCTA
                                                                                                         |  | ||  |||      | | |      |||  | |    |||||| ||  | |||    | |    || | | |||||| ||     | | |  ||||||| ||||| || |||||||| || || ||||| || || ||||||||||| || |||||  | |||||||| ||||| || || || ||||||||| 
-------------------------------------------------------------------------------------------------------taaaatttgttttgtatactttgctcatacttaggttacacacatttcaatttatttatcttatcaaaaagcatggatttgacattctcactgatctcagAGTCCAAATGGTGTCTGGAACATTTTTGGTGGCAAACTTGCATGGGGACCTGAAGCAATTGTTTGTGATGATCCGAATTTCCAGGGACGTGGAAATCCTT
















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|162180535|gb|FC356177.1|FC356177
EST:     GTTCTTGGAGACGTAGTTCTTAATCATCGTTGTGCACAGAAGCAG                         AGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCT
genomic: GTTCTTGGAGACGTAGTTCTTAATCATCGTTGTGCACAGAAGCAGgtaatgcagg ... tgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCT
EST: gi|162171456|gb|FC346731.1|FC346731
EST:     GTTCTTGGAGACGTAGTTCTTAATCATCGTTGTGCACAGAAGCAG                         AGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCT
genomic: GTTCTTGGAGACGTAGTTCTTAATCATCGTTGTGCACAGAAGCAGgtaatgcagg ... tgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCT

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), 32 (downstream exon)
Score: 5

GTTCTTGGAGACGTAGTTCTTAATCATCGTTGTGCACAGAAGCAGgtaatgcagg ... tgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCTGAGGCTATTGTAGGGGATGATCCCAATTTTCAAGGGCGGGGAAATCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcagttctatatgaactgacgttgcgtagctttgacgtttatgatcaccagAGTCCTAATGGAGTATGGAACATATTCGGAGGCAAGCTCGCGTGGGGACCTGAGGCTATTGTAGGGGATGATCCCAATTTTCAAGGGCGGGGAAATCCTA
        ttctatat  TA-rich tract