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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT

Basic information

species Physcomitrella patens
transcript PP1S52_55V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 7
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtga--gatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
                       ||||   | |   |     | || |||   |||        |      |||  | || |      ||  | |  |  |||| ||||| || || |||||||| ||||| |||||| | || ||| | ||||| ||||| |||||||| ||||| ||||||||||| ||||||||  | |
----------------------gtatgatcact-cattaccagatactcacacgaacattgccattgtctgttgtacctaatcttttgttctattattatagGTAAAAGGAGAACCAAATATTTCTTACATCTGTTCAAGGTACTACAGAGCTCCAGAGCTCATATTTGGTGCTACTGAATACACAACAGCGATTGATGTTT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 6
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttg-aatgcgtgggtgcagcattgatcatagtgag-------atttga--gttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
        |       |||| | |   | | || | |  |    |||   | || |||||     | | |   | ||  |  |  |       |||  |  | || |||||| ||||| ||  | || || ||||| || |||||||| |||||||||||||| || ||||||||||| || || |||||||| ||  | ||||| ||||
--------atcaac--ctcacattgctgtatttcttttttcttttatattgctgtaatgcaactctactgtcctcattttgatctgcttttccattcaatcgctgggcagGTTAAAGGTGAAGCAAACATATCGTATATATGTTCACGTTATTACCGTGCTCCAGAACTGATATTTGGGGCAACCGAATACACGACATCAATTGATATAT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
gagtctgcagtggttgctcataatatgga-aattgtctcgtgcggtattcagttgaatgcgtgggtgcagcatt--gatcatagtgagatttg--agttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
        | | |||   | || | | |    || ||  ||       |   | ||||   |   |    ||||   ||| || |    ||    | |||  ||||| ||||| ||  | || || || || || |||||||| |||||||||||||| ||||| |||||||| || || || ||||||||  | ||||| || |
-----cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 6
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcat--tgatcatagtgagatt-tgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
   |  ||  ||  |        | ||    || ||  ||       |   | ||||   |   |    |||  | ||  |||| |  |    | |||  ||||| ||||| ||  | || ||||| || || || ||||| |||||||||||||| ||||| |||||||| || || || ||||||||  | ||||| || |
---ttcgctttgtgtagcatagttttgttgcttttcaagtttctggatatatggaatatatattttactcattttaattctagttaattcacaatttgatcagGTCAAAGGTGAAGCAAACATTTCATATATATGCTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACCGAGTACACAACATCAATTGATATTT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G043350_T02 (Zea mays), 3'ss of exon 5
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
      | |||  |  |  |  || | | | |    |  | |  |  |   ||   | |     |       | ||| |    | ||   |      ||| | ||||| ||  ||||||| || || || || ||||| ||||| |||||||| ||||| |||||||| || || |||||||||||  | ||||| ||||
tcagagggagtactctccaaacattttgcattccaatacttctctgattttttttgttcagaactttgaatcttatctttaaaatatgccaacatatcagATTAAAGGTGAAGCTAATATATCATATATATGCTCACGCTATTATCGTGCTCCTGAGCTCATATTTGGTGCAACTGAATACACAACATCTATTGATATAT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
        ||   ||| ||  | |       |||  |  ||     | | |||   ||       |   |||  ||      | | ||  | ||   ||||||||||| || |||||| |||| ||||| |||||| |||| ||||||||||| || || |||||||| || || ||||| |||||||| || || ||||
-----gtaagatattgatctaagtgctctg-ttggttaatggaagctactgttttttgtcctcaagtttcatccat------gtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
            | |  | ||  || |     |||    ||  | |  |   ||  |   ||    ||   || |||    || | ||  | ||    |||||||||| || |||||| |||| ||||| |||||| |||| ||||||||||| || || |||||||| || || ||||| |||||||| || || ||||
--------gtaagatattgatc-taagtgctctgttagttgatggaagctactgttttt-tgtcctcaagtttcatcc--atgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 7
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
         |||  | |   ||   |   ||||    | |  |    |   |||| ||  ||  | | |  || || ||  |     |||  || | |||||    || || || || || ||||||||||| || ||||||||  | ||||| || || |||||||| || || |||||||||||||| ||||| || |
---------gtgagttcctttaccttctgaatttgaacttttgaagatattttgattgtatgc-tcctgggtttatgatctta----ttgcatttt-cagGTTCCCGGTGAACCCAACATATCGTACATTTGCTCTCGATATTATAGAGCTCCAGAACTTATATTTGGGGCAACTGAATACACAACTGCTATTGATATGT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 7
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
         ||   | |   ||   |   ||||    | |  |    |   ||||  |  ||  | | || || || ||| |||   |||  || | |||||    || || || || || ||||||||||| || ||||||||  | ||||| || || |||||||| ||||| |||||||||| ||| ||||| || |
---------gtaagttcctttaccttctgaatttgaacttttgaagatattttgatcgtatgc-tcctgcgtttatgata-tga---ttgcatttt-cagGTTCCTGGTGAACCCAACATATCGTACATTTGCTCTCGATATTATAGAGCTCCAGAACTTATATTTGGGGCTACTGAATACACAATTGCTATTGATATGT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 7
---------------------------gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
                           | || ||     ||   |  ||   |      |  ||| ||     |||||||   || |||| | || | ||| |     | |  |||||      ||||||||||| || || ||||| |||||||| |||||  |||||||  | || || ||||| ||||||||||| || ||||| || || || |||||||| |
gtatgttttatgtacgtatgtgtgtgtgtgtgtgtttctgtcttttctaccttcacgcattcctcttgaaac-ttcagttatctgggtggtttcacc-ttgtttgctctaacctttga------cagGTGAAAGGCGAACCAAATATATCGTACATATGTTCTAGATATTATAGAGCACCTGAGCTTATATTTGGAGCAACTGAATATACTACAGCTATTGACATTT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 6
gagtctgcagt-ggttgctcataatatggaaat-tgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtg-cagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
 | | |  ||  |   | ||||    |||       |        |  |  ||||   |||         | || |||  || | |  |||   |  || |||||| | || ||  | || ||||| ||||| |||||||| || || ||||| || ||||| |||||||| ||  |||||||||||||| |  |||| || |
caatatatagaagaaaggtcattggttggggtcacatgctaatttgcttatagttatttgctcataaaaggtat-gattttaataa--tttatttcatgtcagGTGGAGGGTGAATCAAACATTTCATACATATGTTCACGGTACTATCGTGCCCCAGAGCTAATATTTGGTGCGGCAGAATACACAACTTCTGTTGATATTT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggta-ttcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
                   | | | |   |  | |  |     ||  || ||||   | | | |     || | ||| ||   | |   ||   |   ||||||||||| || || |||||||| |||||||||||| |||| || ||||| || ||||| || |||||||| || || ||||||||||| || |||||||
-----------------gtaaagtttatcagctatagctcttagtggtttagtt---ttcctagtccatgcttagattatgacgtgtcatgg--tccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv14s0066g01050.t01 (Vitis vinifera), 3'ss of exon 7
------gagtctgcag--tggttgctcat-aatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
      |  |  |||   |  || |  || ||||   | | | ||  || |  |||    |  ||||| ||        |||| |  |  |     ||   |    ||||| ||||| ||||| ||||| || || |||||||| || ||||| || || || || || |||||||| || || || ||||||||||| |||||||| |
ctttttggctaagcaccttatttacctatcaataaatataatttcctgtaccttatcatatgtaatgcatga-------attgcttctgatccatcttttataa--cagGTTAAAGGTGAGCCAAATATATCATATATTTGTTCTCGTTATTATCGAGCACCAGAACTCATATTTGGTGCAACGGAGTACACAACTGCAATTGACATGT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
         |||| |||| | || || | |    |       || ||||||  |      || ||       |  || | |  | |           ||||||||||| ||||| || || ||||| || ||||| || |||||||||||||| || || |||||||| || || || |||||||| || || ||||| |
---------gtgggtgcttacaa-ataggatcctt-------ggaattcagcagctgatttgcgtttcctgcttttcttggcaaaac-------aaacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

upper sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 6
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
                                        | |   | | || |||| | |   |    | ||     ||      |||  ||| |  ||||||||||||| || || || || ||||| |||||  |||| ||||| || ||||||||||| || || || || ||||||||||| || ||||| || |
----------------------------------------gtga-gtgctgtcgaattcctttctttcacgtttgatgtaaacttgttttggttttttagGTGAAAGGGGAACCGAACATCTCTTACATATGTTCCAGATACTACCGAGCGCCCGAGCTGATTTTCGGTGCCACGGAATACACAACAGCAATTGATATCT

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|162199400|gb|FC373741.1|FC373741
EST:     CCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTG                         GTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCT
genomic: CCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTGgtgagatgtg ... agttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCT




















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: 24 (upstream exon), 31 (downstream exon)
Score: 6

GTGAATCCCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTGgtgagatgtg ... agttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
                        cattgat  putative branch site (score: 6)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagca