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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaggatttgaaacaggctcgactgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG

Basic information

species Physcomitrella patens
transcript PP1S28_307V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
tcaggatttgaaacaggctcga-ctgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG---
                | |||  |||  | || | | | |   | |     | | ||| |   ||  ||  |||| ||||  |  ||||  ||| |    |     ||||| || || ||||| || ||||||||||||||||||||||||  |||||||||||| ||||| |||   |||| ||||    |  | || |    
----------------gttcgctctgttcaatttctctaacacgttcttacttt-tttgctgctctcttcattgt-cttacattgtgtgcattgaa--ttgcagAGATGGCTAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCACAAGAATGGCATCAAAAAGCCAAAGAGGCACCGCCACACTTCCACCAA

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
tcaggatttgaaacaggctcga-ctgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG---
                | |||  ||| || |  | | | |  || |     | |||| |  |||| | ||  | |  | |  |  ||||  ||| |    |     ||||| || || ||||| || ||||||||||||||||||||||||  ||| |||||||| ||||| |||   |||| |||     |  | || |    
----------------gttcgctctgtgcaaattctctaacttgttctcactttgttga--tttcctcttcatttcgtaacattttgtgcattgaa--ttgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
tcaggatttgaaacaggctcgactgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG-
                |  |  |  |  ||| | ||||       |  |  || ||| | |  | | |   || | |  |   || |   |  |  | ||| | ||||||||| || ||||| || || || |||||||||||||||||   |||||||||||| ||||||||       ||||||    |  |||| |  
----------------gtacagcctctgcatct-tttggtaaaacgacgccgtttttgc-tcccatctcactgaattcttccactttcaat--gctgtagGGA-AATGGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACC

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|162230925|gb|FC407180.1|FC407180
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|7147989|gb|AW509911.1|AW509911
EST:     CTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|7287274|gb|AW599761.1|AW599761
EST:     TCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: TCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|67694976|gb|BJ955209.1|BJ955209
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|18352170|gb|BJ184224.1|BJ184224
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|7047097|gb|AW476998.1|AW476998
EST:     GCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: GCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|37827441|gb|BJ585453.1|BJ585453
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|18338608|gb|BJ170632.1|BJ170632
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|7207648|gb|AW561588.1|AW561588
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|18348071|gb|BJ180118.1|BJ180118
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|18346549|gb|BJ178594.1|BJ178594
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|67571625|gb|BJ944449.1|BJ944449
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|18358137|gb|BJ190196.1|BJ190196
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|37831859|gb|BJ589871.1|BJ589871
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|67569327|gb|BJ942151.1|BJ942151
EST:     TACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: TACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|37825658|gb|BJ583724.1|BJ583724
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|67692587|gb|BJ952820.1|BJ952820
EST:     GCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: GCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
EST: gi|7583117|gb|AW699281.1|AW699281
EST:     CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAG                         GTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA
genomic: CTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGA

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: 115

CTCTTTCTCCTTCCTTCCCCCTCGCGTTGCCTTTGCTCTTCTTCCTGAACTCGCCGGAGTGTCTGCTTGCAGTACCTCCTCCTTCAGgtccctcttc ... ttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG
                    ttttgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaggatttgaaacaggctcgactgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC