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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactcaccgtatccgattcctgcgaacttgaactatatgtgcatagacctgacttctcttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC

Basic information

species Physcomitrella patens
transcript PP1S100_191V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 2
gtacgtactcaccgtatccgattcctgcgaacttgaactatatgt-gcatagacctgacttctcttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC
                | | | |  |    |  || | | | ||| ||||  |  |  ||  | |  |  |   ||         |  ||   ||  |||| ||| |||||  | | ||||||||||||| |||||||||||||||||| |||  ||||  |||||  |  |||| ||| |  | ||  | || || || ||  | ||| |  | ||| 
----------------tgcaagtattttttatgtgcattttctgttgcatgtatttacctcgtatagtggaaggtaaaaggggaagaatttttaa--tgaatattcattttact-caagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT

upper sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 4
gtacgtactcaccgtatccgattcctgcgaacttgaactatat-gtgcatagacctgacttctcttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC
              |||  | |    |  |||   |  |  ||  || | |||  | | |    |  |  |  || |  |||||  | |||           || | | || |    |||||||||||||||| ||||| ||||||||  |||||||||  |||||| |  |  | |||||  | ||  | ||| |||| || || ||| |  | ||| 
------------aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagatttt--acatcaat-ttagttttaaatctatggctcttta----agTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT
















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|162164460|gb|FC341573.1|FC341573
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTNCA-GGTTTCAACTGGGAGAGCTGG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTT-CAAGGTTTCAACTGGGAGAGCTGG
EST: gi|162277582|gb|FC453525.1|FC453525
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162183700|gb|FC359096.1|FC359096
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162164680|gb|FC340727.1|FC340727
EST:     ATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: ATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162245206|gb|FC422135.1|FC422135
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162150325|gb|FC326597.1|FC326597
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162198198|gb|FC372589.1|FC372589
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162166456|gb|FC342438.1|FC342438
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162191940|gb|FC366945.1|FC366945
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162254706|gb|FC430995.1|FC430995
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
EST: gi|162171142|gb|FC347756.1|FC347756
EST:     AATCTGGGACAGGATCTGGCCGCGAGATTGTG                         TTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG
genomic: AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATG

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: 26 (upstream exon), 31 (downstream exon)
Score: 8

AATCTGGGACAGGATCTGGCCGCGAGATTGTGgtacgtactc ... ttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC
                                      attgatttt  TA-rich tract