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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattttttttgggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT

Basic information

species Physcomitrella patens
transcript PP1S459_11V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g24690.3 (Oryza sativa), 3'ss of exon 2
taattttttttgggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
         ||   |  ||   ||  |||| |     |||    |  | |  ||| | ||||  |     |  |||  || | ||| | || |    ||||||||| ||    ||||||||||||||||  || ||  |||| |||||||| ||||||||||||||||| || || ||||| ||| ||          ||
--------gttattaactcaccttcctttgttcatggctgaatacgcttcattct-gtatgttgacaacttggtgta-tcgattttctgtaata---cagGCCTGACGGCAAGAAGAAGGCTTACGTGAAGCTCACTCCAGACTATGATGCTCTTGATGTGGCCAACAAAATTGGCATCATTTAAGTTAGGGCGCTTTTT

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g42270.1 (Oryza sativa), 3'ss of exon 3
taattttttttgggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTC-TGTTCAATT
         || | | ||    || ||   |  |||  |  || | |   |  |||||  ||| | ||             |   ||  | | ||| ||||||||||||    ||||||||||||||||  |||||| |||| || ||||| || || |||||||||||||| || ||||| ||| ||    || |  |  
--------gttagcactttcc-ttcat---acttcattttatcgcttgatttgctaggtagtgtagtt--------aactgaccctacttgtcttc-cagGCCTGATGGGAAGAAGAAGGCTTACGTGAAGCTGACACCAGACTACGATGCTCTCGACGTGGCCAACAAGATTGGCATCATCTAAGTTAGGGTGCTGCAG-

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G083253_T04 (Zea mays), 3'ss of exon 3
taattttttttgggatttcgta-ttgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatc-tattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
                || | | |||      | | |  | ||||    |   | ||  ||||       |||| |  || |   ||||| | | |   ||||||||||||    ||||||||||||||||  |||||  | || |||||||| ||||||||||||||||| ||||| ||||| ||| |  |   ||     
---------------gttagcacttgccccagtgtaattttttcctgcacgatt-tattatgttgtgcaactaaag-agttattcttatcgtgtctgtgcagGCCTGATGGGAAGAAGAAGGCTTACGTGAAGCTGACTCCCGACTATGATGCTCTTGATGTGGCCAACAAAATCGGAATCATCTAAGTGCTGCATTAGGCA

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G124411_T04 (Zea mays), 3'ss of exon 3
taattttttttgggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaat-gtggtcaaatttatctattttctc-agGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGT-TCAATT
         || | |||| ||   |  ||  | ||   ||    |||   |   || | |||| || |   | |  |  |  | | | ||| |  | || ||||||||||||   ||||||||||||||||  || |   | || |||||||| ||||||||||||||||| ||||| ||||| |||| || | |  |||   
--------gttagcatttggtccagtgttattttcttgtg----cataatttattatgttgtgcaactgtgagttattcttgattgtgtctgtcctgtccagGCCTGATGGAAAGAAGAAGGCTTACGTGAAGCTTATGCCTGACTATGATGCTCTTGATGTGGCCAACAAAATCGGCATCATCTAAAGTTACCGCGTCAGG-

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G166659_T01 (Zea mays), 3'ss of exon 3
taattttttttgggatttcgtattgatttgatatcacctgtt-cccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT-
             | |  ||  ||| |    | | |  | ||   |||   |   ||   |||| || |      ||| |    || || | |     ||||||||||||    ||||||||||| |||| ||||||| | || || ||||| ||||||||||||||||| || || ||||| ||| ||    |  ||| | 
-------------gttagcgctttgctccagtgttattttttgtgcataatttgttattttgtgcaact----gagtgattc--ttgatgtgtccatgcagGCCTGATGGGAAGAAGAAGGCTTATGTGAAACTGACACCCGACTACGATGCCCTTGATGTGGCCAACAAAATTGGCATCATCTAAGTTAATAGG-CAACTG

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G40780.2 (Glycine max), 3'ss of exon 2
taattttttttgggatttcgtattgatttgat-atcacctgttcccattcctctctaggatg--tgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
||  | |     ||     | |   |     | || |     |  |||||     ||  |    ||  ||||||  ||   |  ||||| ||| ||    ||||||||||||| |||||||||| || || ||  ||||| | |||||||| || || ||||||||||||||||| || || || |||| |      |    |
taggtataacaaggcaaatgaaacaacaaatttatgaaaaacttgcattcaaacttacaacagatgccatttcttctgaattttaatttttctgttg---cagGCCTGATGGAACCAAGAAGGCCTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATATATGGCCT

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
--taattttttttg-ggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
  |    |    ||   ||     |   | ||  ||| |     |  ||||  |   ||  |      ||||||  ||   | | |||| ||| ||    |||||| || ||  ||||||||||||| || ||  ||||| | |||||||| || || ||||||||||||||||| || || || |||| |   |  |    |
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttg---cagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G39460.1 (Arabidopsis thaliana), 3'ss of exon 2
taattttttttgggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
    |  |||   ||    |||||  | |   |   | ||||   |      |     ||||  ||| | |       |    |||   | || |  ||||||||||||| ||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||||| ||||| ||| | |     ||  | 
---gtactttaaaga----gtatttttctatgaagccttgttgtgagattgatt----atgttcaatatatttgacactatggtttggtt-ttgttacagGCCTGATGGAACCAAGAAGGCTTACGTGAGGCTTACACCAGACTATGATGCTTTGGATGTTGCTAACAAGATCGGCATCATCTAAGTCTATCTATCTCTG

upper sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv13s0019g00250.t01 (Vitis vinifera), 3'ss of exon 3
taattttttttgggatttcgtattgatttgatatcacctg--ttcccattcctctctag--gatgtgaaatttctaatgtggtcaaa---tttatctattttct-cagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
          |||  |    ||| |   | ||| ||  ||  ||  |  |      |||  | ||| |||||    || ||  | ||   | ||||| | |  | ||||||||||||| ||||||||||||| || ||  ||||| | || ||||||||  | |||||||| ||||||||||| ||||| ||||| |    | |  ||
-----cagaatggtgtgatatatgggcatcataccaagtggattagcgatgtggcatagtggttgtcaaatt---gatatgaactaaccttctatctttgtgttgcagGCCTGATGGAACCAAGAAGGCTTATGTTAGGTTGACACCGGACTATGATGCCTTGGATGTGGCAAACAAGATCGGGATCATCTAAATCTATATTGCCTTT

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|67726855|gb|BJ977114.1|BJ977114
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67716288|gb|BJ966548.1|BJ966548
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67692531|gb|BJ952764.1|BJ952764
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67718378|gb|BJ968637.1|BJ968637
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|18360735|gb|BJ192798.1|BJ192798
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|162254594|gb|FC429444.1|FC429444
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67569273|gb|BJ942097.1|BJ942097
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAN                         GCCTGATGGANCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|162251536|gb|FC428048.1|FC428048
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67725169|gb|BJ975428.1|BJ975428
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67700327|gb|BJ960560.1|BJ960560
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|162216327|gb|FC392120.1|FC392120
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|162254593|gb|FC429443.1|FC429443
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67576792|gb|BJ949616.1|BJ949616
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|67722485|gb|BJ972744.1|BJ972744
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|37838624|gb|BJ596632.1|BJ596632
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
EST: gi|162251535|gb|FC428047.1|FC428047
EST:     GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAG                         GCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC
genomic: GTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGC

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: 33 (upstream exon), 35 (downstream exon)
Score: 10

TGGTTTTCATCGTGGATGTGCGCGCCGACAAGAAGAAGATCAAAGAGGCCGTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgt ... attttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT
                      ttctaat  putative branch site (score: 10)
                                      tttatctattttctc  putative PPT
                                 tcaaatttatctattt  TA-rich tract