Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccgtcgtcgtgaagtcaaagagttttacttatggcattgagaagcatcagtaaaatagttgaaacccacttattatatgttggtggtggtgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT

Basic information

species Physcomitrella patens
transcript PP1S11_387V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S11_387V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G180331_T01 (Zea mays), 3'ss of exon 2
tccgtcgtcgtgaagtcaaagagttttacttatggcattgagaagcatca-gtaaa-atagttgaaacccacttattatatgttggtggtggtgttgaatagGGGACGGAGTTG----AGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGT-GCATGGGACAATCAGT
   |||    | || |   ||      ||||||     | |||| ||  |  |||| | | |||||    | |  |   ||     |  ||    |  |||     ||   | |    ||||| || |||||||||||||||||||||||||| || ||| |  | || ||  ||| ||| || || ||  |  |||||  | | ||
---gtcacgctaaaatactagcac---acttataatcctaagaaacaagatataaatacaattgaattttattactctgatccatattatgtctctctataaccagCGTCATCGACTTAGAGGTGGACCGCAGATGATTCAGTTGAGCTTGGATGGCAAGAGGATATACGTGACAA-CTCACTTTTTAGCCGTTTGGGATGAGCGGT

upper sequence: PP1S11_387V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 6
---tccgtcgt-cgtgaagtcaaagagttttac-ttatggcattgagaagcatcag--taaaatagttgaaacccacttattatatgttggtggtggtgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT
   |   || |  |||| |   ||  ||  ||| | || ||| | | ||   | |   |  | | ||| ||      | |  | ||     |  |  | ||    |||| |   |||||||||  ||||| ||||||||||||||||| ||||| || |||||  | |||||  ||||||| ||||||||||||||||| || || |
tattttatcttatgtgatgcttaaacgtggtacataattgcactcataattttgaccctttagtggtttaagg----tgaagagatcaaaattttaatttt---cagGGAAATAAGTTGAGAGCTGGCCCTCAGATGATTCAGTTGAGTTTGGATGGTAAGCGGCTATATGTTACAAACTCACTCTTCAGTGCATGGGATAAACAAT

upper sequence: PP1S11_387V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 6
-----tccgtcgtcgtgaagtcaaagagttttacttatggcattgagaagcatcag--taaaatagttgaaacccacttattatatgttggtggtggtgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT
     |   | ||  |    | |||     | | | || ||| |   ||   | |   |  | | ||||||    |     |  |  ||  |  |    ||    |||| |   |||||||||  ||||| |||||||||||||||||  |||| || |||||  | |||||  ||||||| ||||||||||||||||| || || |
tattttatcttgtgttatgcttaaacgtggtaaataattgcactttaaattttgaccctttagtggttgaaggtgaagagatcaaaatttttaat----tt---cagGGAAATAAGTTGAGAGCTGGCCCTCAGATGATTCAGTTGAGTCTGGATGGTAAGCGGGTATATGTTACAAACTCACTCTTCAGTGCATGGGATAAACAAT

upper sequence: PP1S11_387V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 6
tccgtcgtcgtgaagtcaaagagttttacttatggcattgagaagcatcagtaaaatagttgaa---accca-cttattatatgttggtggtggtgttgaat----agGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT
       | | |||  | || | | |||  | ||       ||   ||   |   | | |  |    | | | ||  | |   | || || |    ||   |    |||| |   |||||||||| ||||| ||||||||||| ||||| || || ||||||||  | ||||   | ||||| || || ||| | |||||||| || |
-------ttg-gaacaccaatattattatatctgatgcatggatttattcttttgacattcaagggtatctatctcgtcagtggctgatgttaacattcctttttcagGGAAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAGCGGCTCTATGCTACCAACTCACTATTTAGTACTTGGGACAAACAAT

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|162161906|gb|FC338281.1|FC338281
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|162174753|gb|FC352169.1|FC352169
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|162151131|gb|FC327650.1|FC327650
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|162212622|gb|FC389014.1|FC389014
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|162189384|gb|FC366542.1|FC366542
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|162268196|gb|FC443874.1|FC443874
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|208353106|gb|DC921850.1|DC921850
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|208384431|gb|DC928182.1|DC928182
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|37845309|gb|BJ603317.1|BJ603317
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGCCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|208374862|gb|DC956135.1|DC956135
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|208359243|gb|DC954166.1|DC954166
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|37830302|gb|BJ588314.1|BJ588314
EST:     AGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: AGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
EST: gi|208382645|gb|DC919813.1|DC919813
EST:     ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAG                         GGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG
genomic: ACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGG

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: 24

CACGGGTCAAGTATGGGTCGGCGGACTAATTCGCAAAGGTGGTAATGTTTACGTCGAGGAGTCGGGTGAGACATGGCAATCAACTGTTCCTGATGTCCAGgtgaactttc ... tgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagtaaaatagttgaaacccacttattatatgttggtggtggtgttgaatagGGGACGGAGTTGAGAGGCGGCCCGCAGATGATTCAGTTGAGCTTGGACGGGAAGCGATTGTATGTCTCAAACTCGCTCTTCAGTGCATGGGACAATCAGT
      taaaatagttgaaa  TA-rich tract