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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA

Basic information

species Physcomitrella patens
transcript PP1S112_186V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
---gta-agaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
   ||  |    | || ||     ||| ||||     | |||   || ||   |  | | |||||         |    |  |    | ||  | ||| |||| || || || || || || |||||||| ||||| || ||||   | ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttg-ttgtatgttctcacaaaattctactgga-tgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
-gtaagaagtcatggtcgttggtg-gattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
  | |  |   ||| |   |  |     | |||||| |||   |    | ||  |  ||| ||  |    ||          ||   ||  | ||| |||| || || || || || || |||||||| || || || ||||   |||| || |||||||| ||||||||||||||||||||||| ||||| ||||| ||
ccttatcatatatgttgcatactacagcttaaatgcatttgttgccattcctatttcattctagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttga----tcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
            |  ||||  | | ||   | |    || ||||  |   ||   || | | |  |||||||  |||||    | | | |  |    | |||||||||| ||| ||||||| || |||||  ||||  | ||||   |||| || |||||||| ||||| ||||||||||| ||||||||||||||||| ||
------------gtacgtttcttgttttggacg----tagagttgttaagggagcat-gcagacttgattattccttgaatgtttacattttggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagaagtcatg-gtcgttggtggattaaaa------tgcttttaaagtttatgctggtcgattgt-----aaaaatgattatctc----ttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
||| |   |  ||  |   || |   | |||       ||| |  |||    | |||  ||  || |      | |   | || |      ||  ||| | |  |||  | |||||||||| ||  |||| || ||||||||  ||||  ||||||   | || ||||||||||| || || ||||||||||| || |||||||||||||| ||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgc-tgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
--gtaagaagtcatggtcgttggtggat---taaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
      | | ||  | |   ||    ||   ||| |||  |||     |  |   | |    |||  ||| |||| |||  | | || |    |  | | |||| ||||| ||  | ||||||||||||||||| || |||||||   | || || ||||| |||||||| ||||||||||| ||||||||||| ||||| ||
ttccttgtattccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaa-gatt-tctaatcaccagataatgact-tgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 4
------gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
       |   ||||    ||  |   |   || |    |||||  |    |  ||| |      | |  |||| ||  | ||  |||    | | || | |||| || || ||  | ||||| ||||| || || ||  |||| |   | || || ||||| ||||||||||| ||||| ||||||||||||||||| || ||
aaaaaccttgaaagtgcctgttatct-tcattttattcacttttgcatggaaatctgctattccctcaggatgactaattttt--tcaggtagtg-gtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTGTTCCCGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
------gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
       |   ||||    ||  |   |   || |    |||||  |    |  ||| |      | |  || | ||  | ||  |||    | | || | |||| || || ||  | ||||| ||||| || || ||  |||| |  || || || ||||| ||||||||||| ||||| ||||||||||||||||| || ||
gaaaaccttgaaagtgcctgttatct-tcattttattcacttttgcatggaaatctgctattccctcaggattactaattttt--tcaggtagtg-gtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgatt-atctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
                              |   ||| |    || |   | |||||    |||   ||| ||  |||||  | |||         |||| ||||| || ||||| ||||| || ||  ||||||| || ||||| ||||| |||||||||||||| |||||||| ||||||||  | || ||||| ||
---------------------------gtgagcttttcactcctttttaagatcgatcactaaacgaatttattacttgactacact---------cagGCAAGACCGTTTTCACGAGCGACCACGCTTTGAAGCTCGAATGGATACCAGATTGGATTGCCATTGTCGGAAGTGGCTACATTGGCTTGGAATTCAGTGA

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgatt-atctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
                                || ||| |    | |   | |||||    |||   ||| ||  |||||  | |||         |||| ||||| || ||||| ||||| || ||  ||||||| || ||||| ||||| |||||||||||||| |||||||| ||||||||  | || ||||| ||
----------------------------gtgagcgtttcactccttttaagatcgatcactaaacgaatttattacttgactacact---------cagGCAAGACCGTTTTCACGAGCGACCACGCTTTGAAGCTCGAATGGATACCAGATTGGATTGCCATTGTCGGAAGTGGCTACATTGGCTTGGAATTCAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
                              tcttgat  putative branch site (score: 4)
            attgtaaaaatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG