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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG

Basic information

species Physcomitrella patens
transcript PP1S66_174V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 12
-----------------------------gtaagtgctcag-----tgattgtttagtgtttctgctt---gttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcat-tggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                             | ||   || ||     | ||    ||   ||||        |||   | | | | | ||  |||      || |    ||  | |   ||||||  | ||||  | |  |||| ||||| ||||| || ||||||| ||| | |||||| | |||| |||||||||| ||||||||||| ||  |||| || ||||| ||||
gtgagtagcttgctccttgtttaactggtggaaaatcttagcaaactaatcacataacttttcaaggcaaagttacatataaggaagctc-ttgtatacattgtcaaatgtgattc--catggttttctggtcatttgaagGAATGGATTATGGACCAATGGGAAAGGAACTACTATATAACTGCACTTGCTGGAGCAAATAATGGGAGTTCCCTGGTAGTGATGTCAAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 12
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttg-gccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
  ||    | | ||||| | ||   |   || |   |  || | |      |||| | |   | | || ||   |   ||||| || |  |   | |  ||  ||| ||||| |||||||||||||| |  ||||||||||||| |||| | ||||| || |||||||| |||||||||||  | ||||| | ||
-caacactttactgattatatatcatcaatgatgtctcattgtcatttgcatagtggtgttttatgctgttacagtttttaacttgcttgt-actgtgtta--gGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 5
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaa-attaacatggtcat--tggtattctac-agGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
          | | | ||||   ||||| || ||||        |     ||  ||   | || ||  |  ||    |||  |||   |||  | ||| | |   |||| ||||| |||||||||||||| |  ||||||||||||| |||| | ||||| || |||||||| |||||||||||  | ||||| | ||
-------aaaatttactgttctttgtttatgattgtacgccaacacttcactgattatacatcctcaatgatgtctcattgtcatttgcatgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                 ||      || |    ||    |  ||     |||  || |   |  ||  || || |||  ||||    ||     |     |||||||||||||||||||| ||||| || | |||||| |||||| |  |||||||  | || ||||| || ||| | || || ||||| ||||
-----------------gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaa-aacaaaaacaaaaaca-----cagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 13
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
           ||      |   |  |  ||| |  || ||||      ||||       ||    || |    |  |  |  ||    ||  |   ||  |||| ||||| ||||| ||||||||||| || | ||| |||||||| || ||||| || |  |||||||| || ||||| |||||||| ||||
-----------gtatggtctcgattctcatgcatagtgctttt------tctaagcaaggctacatttata---agctacaagtgtcttttcttgcactttagGATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 12
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagt-tggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
     || |   || ||   |  |  |   |  ||| | | |   |  || || | |       | ||| |   |  |||    ||||  | | |   ||  |||| ||||||||||| || |||||||| |||| |||||||||||||||||||||||||   || ||||||||  | || || ||||| || |
tctcatgttttctgcttacatgat--tgtagtctgtagatctgttaatatataatctcaaggcatgcttattaagggatt--tttggttttggtttacctgaagGAATGGATCATGGAGCACTGGGAAAAAAATTACTATATCAGTGCAATTGCTGGAGCTGTAAACGGGAGCTCGCTAGTAGTAATGTCTAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 12
---gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
   |||  | ||   |   || ||   || |  | |   ||||  |  |  ||||    |||   | | ||   |||  |||    ||||  | | |   ||  |||| ||||||||||| || |||||||| |||| ||||||||| |||||||||||||||   || || |||||  | || || ||||| || |
ctcgtattt-ctgcttacatgattgtagtcttggatc--tgttaatatataatctcaa-ggcatgcgtattaactggggatt--tttggttttggtttacctgaagGAATGGATCATGGAGCACTGGGAAAAAAATTACTATATCAGCGCAATTGCTGGAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 12
gtaagtgctcagtgattgtttagtgtttctgc-ttgttgtttttgaaggatctagttggccctcttcttttg-tggaaattaacatggtcatt--ggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG-
           |  ||| | |  | | | |   |   |  || | |   |  ||| |  |  | ||| | || || |  ||  |   || |||  | |  | | ||||| |||||||||||||||||||||||||| |  || || | | | ||||| || |||||||||||||||||| | || || ||||| |||| 
----------tgaaattatatgatttatataaatcagtacttgtcatataattagctatctgttttcatatgatgaatcttgcccatgtgattctgtttcttttcaggAATGGATCATGGAACAGTGGGAAAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTTGTGGTGATGTCAAAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
              |  | | |    ||  | |   | | | ||    | ||| |    |     || | |  |      |  || |  | | |  | | ||||| |||||||||||||| ||||||||||| | |||||||||| | || ||||| || |||||||| ||||| ||||| || ||| | ||||
---------gtaaaacagctgaagcattaggatccatctatctgtcatacctatt----ctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G03930.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
|||    |    ||     |   ||| |   ||   | | | |  || | |   |   | || || |||| |           |  | || | |  |   ||||| ||||| ||| |||| ||||| ||||| | |||||||||| | || ||||| || |||||||||||||| |||||||| ||||| ||||
gtattaccatcatgtccact--atgtatgctctgactatatatatagtagcagctcaccacttttttttttt-----------tttttatggattcttggcagGACTGGATTATGAAACAATGGGAGAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGGAGCTCATTGGTCGTTATGTCAAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                             |  |  | | ||  |||| || |||    |  ||   |||     || | | |||   ||||  |  |   ||||| ||||| |||||||| ||||||||||| | |||||||||| | || |||||  |  |||| |||| ||| || || || ||||| ||||
----------------------------gtaataatcgctt--gaagcatataggaatcaatcaattttatattaactcaccatttgcatt--ttcttggcagGACTGGATTATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTTCAGATAACGGGAACTCATTAGTTGTTATGTCAAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------------------------------------------gtaagtgc--tcagtgattgtttagtgtttctgcttg--ttgtttttgaaggatctagttggccctcttcttttgtgga------aattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                                                                ||| |    ||||| ||  |  ||   |  | |  |  |  || ||  ||  |   |||   | | |  ||||    |      ||||||  |  |  |      |||| |||| ||||| |||||||||||||| || || ||||||||||||||||| || ||||||| ||||||||||||  | || || ||||| || |
gtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagt-atgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
        | | |  || |   |||||  |   | || | ||    |  |   |||    |    ||  |                |  | | | |||   |||| ||||| |||||||||||||||||||||| ||| |||||  |||| || || |||  ||||||||| |||||||| |||||||| ||||
-------gttattttttttcatgtgttgatttctattatcttctgtgagtg-ggttcatgcatacctgatactactgacctttcacttttggattttcactagGATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 12
-----gta-agtgctcagtgattgtttagtgtttctgctt-gttgtttttgaaggatct----agttggccctcttcttttgtggaaa-----ttaacatggt-cattggtatt--ctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
      || | | || |       ||   ||||    |||  |||      | | || |    |  |||| |     || ||| ||||     |||| |  ||   || || ||  ||  |||| ||||| |||||||| ||||| ||||| |  || ||||||||||| || |||||||||||||||||||| ||||| || ||||| || |
gttgcttatattccttaacaggcattgcatgttagcacttcattgaacagtatgcatgtcacaaactggcacgtaaattgtgttgaaaacaagttaatactgtatttttgtctttgctgaagGAATGGATTATGGAACAATGGGAGAAGAACTATTACATCAGTGCAATAGCAGGAGCTAATAATGGGAGCTCATTGGTGGTGATGTCCAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv11s0016g04060.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaa--ggatctagttggccctcttcttttgtggaaattaacatggtcattggtat--tctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
||  ||||| |   |    ||     |   || ||   | ||  |    ||| || |         ||    ||  |||     ||      || | |  | | ||||||||||| |||||||||||||| ||||| |||||||||| | |  ||||||| || |  ||||| |   ||||||| || ||||| || |
gtgggtgctaacaaagctctttaccatgaggcatgacctcttgcagtttgattta-tcaaaaaatatccagggtaaaaaagcttattccttctgatttcattttcagGAGTGGATAATGGAACAGTGGGATAAGAACTTCTATATCACTTCCGTTGCTGGTGCAAGCAATGGCAATGCTTTGGTGGTAATGTCAAAGG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                                                   |||     | |  |    | | | |||   ||| |    |  |  ||  |||||||||||||||||||| ||||| || || ||||| || ||||| ||||| ||||| || || || |||||  |||| |||||||| ||||
-------------------------------------------------gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

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|162189086|gb|FC365204.1|FC365204
EST:     CAGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAG                         GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
genomic: CGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
EST: gi|162194954|gb|FC369032.1|FC369032
EST:     CAGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAG                         GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
genomic: CGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT

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: 34 (upstream exon), 35 (downstream exon)
Score: 29

CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
                           aattaac  putative branch site (score: 29)
                          aaattaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT