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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaagagaatgaaagtcctcttcattactctggatctgattgttttaagtcttgttttttaacattgattatttatttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG

Basic information

species Physcomitrella patens
transcript PP1S456_6V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
--taaga--agagaatgaaagtcctcttcattactctggatctgattgttttaagtcttgttttttaacattgattatttat-ttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG
|| | | || || || ||| | | | || | || | | || | | |||| | | | || ||| | | || ||||| ||||| |||||||| || || || || |||||||| | |||||||| || ||||||||||| || || ||||| || ||||| |||||||| || |
tccaatgtcatatgttggggtacccgtttatttcacagtattc--tcaccagaaat-tggtataagcatattgttgaaatgcgctaattgagct--ttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG

upper sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 7
-taagaaga--gaatgaaagtcctcttcattactctggatctgattgttttaagtcttgttttttaacattgattatttatttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG
||| | | || | | | | |||| || || | | | | ||||| || || || ||| | | | | | | || || ||||||||||||| ||||| || || || |||||||| ||| ||||||| |||||||| ||||| ||||| ||||| || || ||||| || ||||| || |
gtaaaatccctaattgctactaatgtgaattatcctcgacagaaaatataagaatgttgttgttcaagatgttttaagtttctggtcctat--ctcaacgtagGTATTGATAGGTAAAATCTCAACGGGTGCGCAGAACGATCTAGAGAAGGTGACGAAGATGACTTACGCGCAAGTAGCTGTGTATGGTTTCAGTGACAAGG

upper sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 7
-----taagaagagaatgaaagtcctcttcattactctggatctgattgttttaagtcttgttttttaacattgattatttatttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG
| | | || | | | | || | |||||| | || | | ||| || |||| | | ||||| ||||| || | |||||||||||| || || |||||| | ||||| || || || |||||||| || || |||||||| ||||| |||||||| || |
atatttgcttacaatattagaaaagaaaagacgaacctctagtgttttgtttcagtgtttccgccgtgatgatgacagg--gttcatttcctatgg---atgcagGTTTTGATTGGTAGAATATCGACAGGAGCCCAAAATGATCTGGAGAAGGTAACAAAGATGACATATGCTCAGGTCGCAGTCTATGGTTTTAGTGACAAGG

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|162150479|gb|FC326127.1|FC326127
EST:     AACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAG                         GTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTG
genomic: AACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAGgtattggacg ... cttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTG
EST: gi|162255777|gb|FC431437.1|FC431437
EST:     AACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAG                         GTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTG
genomic: AACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAGgtattggacg ... cttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTG

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: 3

AGGTTTTGCTCAATATTTACCGAACGAGAATCTGCTCATGACAAAGGAGCAACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAGgtattggacg ... cttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtcttgttttttaacattgattatttatttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG
                                          ttacttc  CT-rich tract
 ttgttttttaacattg  TA-rich tract