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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

Basic information

species Physcomitrella patens
transcript PP1S33_218V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
--gca-ctttttagtcattctagtctg-cagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
    | || |||  | |   |  | || ||    |       |||| |  ||| |       |  |   ||| | | | |   | |  |   |   | | ||||| |||||||| ||||  ||| | |||||||||||  ||||||| ||||| ||||| |||||||||||||||   ||  |||| ||||| ||||| || ||
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattga-actcaacatgtcttctcact---tattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os06g37440.1 (Oryza sativa), 3'ss of exon 7
gcactttttagtcattctagtctgcagagtcaga-gtgtttctctcatgtctcggacgtttggggctga-tagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
 |   || |    ||| ||| |   | | | ||   ||    |    | |  |      |||    ||| |    ||  |  ||      | ||| |  |||| |||||||| ||||  ||| | || ||||||||| ||||||||||||| ||||||||||| || ||||||   ||| | |||||||| ||||| || ||
-cttcttgttacaattttag-caatatatttaggcatgaacttaatttattccattttcttgtttttgaattaacagagacattatcacgtctatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACTACAAGTACAACGATGAGAACACCGTATCGTTTGTGACGATGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
---gcactttttagt-cattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
   |  || | |  | ||   |  | |      |        |||| |   || |     | |  |   ||      || ||  ||     |  | | | ||||| |||||||| ||||  ||| | |||||||||||  |||||||||| || ||||| |||||||| ||||||   ||  |||| ||||| ||||| || ||
ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttc----tcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G122871_T02 (Zea mays), 3'ss of exon 6
-gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcgg---acgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
 ||    |  |  ||   || |    |||   |  |  |   | || | || | |   | ||||| ||    |  ||| ||| |    |   ||| |||  |||| |||||||| |||| |||| | || || |||||||||||||||||||| |||||||||||||| ||||||   ||  ||||||||||  |||| || ||
ggcgtactgcaagcaaattaattgttagatgaattgcttggatttcctttccctgttcatgtttgtggactct--tgacctagt--aatccgtgtgtgtttcagGTTTCTGGGACATGTACGACCCAGAGGGCTACTCTTTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 7
gcactttttagtcattctagtctgcagag-tcagagtgtt-tctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtgg-cagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
      ||||  ||  | | |  || |   ||| ||| || | | | || | |  |  ||     ||  |     |   || |         | | |   |||| |||||||| ||||  ||| | || || |||||  ||||||||||||| |||||||||||||||||||||  |||  | |||||||||||||| || ||
---gcatttaaacaccccattaagcggttctcaaagttttgtttttgatctgttagtagtgctatgcacaagtcaactgaactcaactcccatgtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G122871_T03 (Zea mays), 3'ss of exon 6
-----gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcag-
             || || || | ||     || |   |||       | |   | | | |   |  |  |||   ||| | |  ||||||| |   ||  || |  |   ||| |    | || || |  ||  | | | ||| |  | || |||| |    |    |   ||| | |      |   | |  ||| | | |        
cgacccagagggctactctttgtggttctgtgactacaagtacaatgatgagaacaccgtctcctttg--tgaccctgaacaaggttggtggattcctgcagCGGATGGACCTGTGCCGCAAGTACGCCTTTGGGAAGATGCTCGTGATAGGCTCTGAGCCACCCTTCAAGCTGAAGGGCCTTTGGCT-CTTCCGTGGCCAGG--------

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G059580_T03 (Zea mays), 3'ss of exon 5
-------gcactttttagtcattc-tagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
       | |||  ||    |||  |   ||| |  |   | || || || || | |  |     | ||| |     |   |  ||||  |     | |||||  |||| |||||||| ||||  ||| | || || |||||| ||||||||||||| |||||||||||||||||||||   ||  ||||||||||  |||| || ||
agagggagtactgcttgtaaattaattagctggatggcttgggt-ttcctttccttttccatgtttgtggagtcttgaccaa--taatccg-----tctatgtttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCTCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 7
gcacttttta-gtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttgg-tggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
    ||  ||  || || | || |    ||            | | || | || |  ||     |     |   |   || |       |  | | |   ||| |||||||| |||| |||| | || || |||||  ||||||||||||| |||||||||||||| ||||||  |||  | |||||||| ||||| || ||
--gtttggtatatctttttggtgttttaagcagttcctaagttttgatctgtcagtagtgcaatgtacgaaccaactgaactcaaactctcatgtattttagGTTTCTGGGATATGTACGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACAGTGTCGTTTGTGACCATGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G00360.1 (Glycine max), 3'ss of exon 6
gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
      | ||   |||||| | ||  |     ||  | |    | |||    | || |         ||  | | |   ||   |   |  || | |||||||| ||||| |||| |||  | || || || ||| ||||||||||||||||||| |||||||| ||||||  |||  ||||||| ||  | || || ||
-----gtataactattctattatgatggcaatgatggatatgatgatgagatgcacatc--------attttaatccttttcctt---ttaattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACACAGTTTCCTTTGTTACGTTAAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G28670.1 (Glycine max), 3'ss of exon 6
gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
      | |||  |||| | |||     |   |  ||  | |   |||  |  | | |||    |          ||  |||     ||  || | |||||||| ||||| |||| |||  | || || || ||| ||||||||||||||||||| |||||||| ||||||  |||  ||||||| ||  | || || ||
-----gtatagctattc-attctattatgatggcatggatatgagatgcat--gtcattttaatc----------ctccttttaaattttaattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACTCAGTTTCCTTTGTTACATTAAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
---gcactttttagtcattctagtc-tgcagagtcagagtgtt--tctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
       |  | |||   | | ||    | |  |   | |  |  |   ||| |  |   |  ||||  | | | | |||  ||  ||  || || |     |||||||||||||| |||| |||  | || || |||||| | ||||||||||||||||| ||||||||||||||    ||  | || || ||| |||| || ||
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaa-tatgttcatgattat-----gcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv12s0035g01120.t01 (Vitis vinifera), 3'ss of exon 3
---gcactttttagtcattctagtctgcagagtcagagtgtttc---tctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
       |  | |||   | | ||        | |     | ||     ||| |  |   |  ||||  | | | | |||  ||  ||  || || |     |||||||||||||| |||| |||  | || || |||||| | ||||||||||||||||| ||||||| ||||||    ||  | || || ||| |||  || ||
gcctagttgataagttgctatggttgctctgtttactacttctcattcttcaaggtttaaaactttgaagttcacaatgaa-tatgttcatgattat-----gcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGCCGAGAATACCGTCTCATTCGTAACTCTGATCAAGGT

upper sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
gcactttttagtcattc-tagtctgcagagtcaga-gtgtttctctcatgtctcggacgtttggggctgatagtgagctaat--ttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
   | |     ||||||  | | || |   |  || ||       ||| || | | | |||      || |  |    | ||  | | |   | | | |||||||||| ||||| ||||  ||  |||| || |||||| | |||||||| ||||||||||||||||| |||||    ||  | ||||||||| |||| || ||
--gcctgaagttcattcacaatttgaatgttttgatgtagggtattca-gttttgcatgttccata-tgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT

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|208396917|gb|DC920457.1|DC920457
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|37853516|gb|BJ611524.1|BJ611524
EST:     GGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|37827683|gb|BJ585695.1|BJ585695
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|37826393|gb|BJ584405.1|BJ584405
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|208361215|gb|DC957684.1|DC957684
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|208352629|gb|DC921924.1|DC921924
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|162158942|gb|FC333983.1|FC333983
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|208350807|gb|DC925938.1|DC925938
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|162242488|gb|FC419182.1|FC419182
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
EST: gi|37835709|gb|BJ593721.1|BJ593721
EST:     GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCG                         GATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT
genomic: GCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATT

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: 14 (upstream exon), 22 (downstream exon)
Score: 1

AATACTCTAGATTTGCTCCCACCTAGTCCAATGGTTCTTGATAACTGGAAGCGTTTATATTCTAACACCAAGGCTAAGGATTTTCATTTGGCAATTAGCGgtgagttcat ... tatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT
                            agctaat  putative branch site (score: 1)
                               taattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactttttagtcattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

- - - - - - - - - - -ctgcaga