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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT

Basic information

species Physcomitrella patens
transcript PP1S98_209V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattc--agctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
|| ||| |    | | | |   | ||| | || ||   |||   |||    |||||  |   ||||     ||     |    |  || |   |         |||| | |||||||||||||| ||||||||||||||||| || || ||||| |||||||| ||||| || 
gtaagatgagcgcgctt-catgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G129209_T01 (Zea mays), 3'ss of exon 1
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
                            |  |     ||| | | |  | ||    || ||    |||| |  |      |  || |||   | |     ||||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| 
---------------------------gtaattagcgagtcagttaaatgcaggcaatgcaat--gcagtgcagctctatatattattgtatgttcaagtgcagGCGGATTAGCCACAGGACGCACCACCAGAACCACGGCCACGTGGACAAGGACGAGTCATGGCATCCC

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G128971_T01 (Zea mays), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacg-cagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
                         |     | |  | |||    | |  | ||   ||| |  |  ||  |  |   | | ||| |   ||  | | |   |||| | |||||||||||||| ||||| || |||||||| ||||| ||||| |||||||| ||||| || 
------------------------gtaggattacccatgtttcctatgctcgttagtttctgtcg--aggatcatcgttgatgttgtaagtgaatggaatttcagGAGGATTAGCCACAGGACGCACCATCAAAACCACGGTCACGTTGAGAAGGACGAGTCCTGGCACCCG

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G074401_T01 (Zea mays), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
  |      |  | | ||    || |  | ||     ||||  || ||   ||| |  |    || ||  |       |   |  |||||   |       |||| | |||||||||||||| ||||| || |||||||| ||||| ||||| |||||||| ||||| || 
--gtaggattaccccatgtttctcatgcttgtt----agtttctgtcgaggattatcgttga-tgtcatggaaccacct---gcctttga-atgccattttcagGAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 2
------------gtgagaagctttcacgtgcccttcttcatcg------tgctgaagttaatgacgta--cattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
             |   ||  ||||| || | |||  || |        |  | | |||  | |   |  | |||   | |  |  ||   |    | |        | |||| ||    ||||| | |||||||||||||||||||| |||||||| || || || ||||| || || ||||||  ||| 
ggtcggttccttttagcaacttttcatgttcactttgtccttaaatttttttttatgtttgttaaaaaatctttggtctgatttaacaacctaaccatttttacaactcatggattttttgcaGGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCC-

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G27190.1 (Glycine max), 3'ss of exon 2
-----------gtgagaagctttcacgtgcccttcttcatcg------tgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgg-gttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
            |   ||  ||||| || | |||  || |        |  |   |||||  |  |   |||   | |  || ||   |    | |  | |  |    |   |     ||||| | |||||||||||||||||||| |||||||| || || || ||||| || || ||||||  ||| 
gtcgattccttttatcaacttttcatgttcactttgtccttaaatatttttttttgttaaaaa-atcttttggtctgatttgtcaacctcaccattttactactcatggatatcttttgcagGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCCG

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
             | |    |||  |  |         | |    ||   | ||||||   || ||| |      |  || | |  | |  | | | |||||    ||    | ||| | ||||||||||| ||||||||||||||||| || || || ||||| ||||| ||||||||||||
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcac-ttgaagaataatatcacattcttcatgacaatatttga-attttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgac-gtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
|||||      |  |   || ||||||      || ||   | |  | | |  |  | |||  |  | | |  | |||       |||             ||||| | ||||| ||||| ||||||||||||||||| || || || ||||| ||||| || |||||||||
gtgagttttgctttcagaccattcttct-----ctaaaaccacttgcagaatctcatcttcttcatgtaaaaatatga------cttt-------------gcagGAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCT

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
---gtgagaagct-ttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
    |  ||   | ||    |   |  |   | ||   | |  | |  || |||  || || |   |     ||  ||| | ||     ||   ||||||  | ||||| | || |||||| |||| |||||||||||||| || || || || |||||||||||||||  ||| 
taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtat-ttataatttacgaattgaaatgttaata-----ttaattgggtt--atgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23113 (Selaginella moellendorffii), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
                              || |  | | |  |     |  |  | ||  |||   |||| |     |||| ||| ||         |  |||| | || |||||| |||| || |||||||| ||||| || || |||||||||||||| |||||||| 
------------------------------gtacgtatgctttt---ccatttcttgtttggct--tagagct-----taaactttgtgg------aaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

upper sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 2
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
                              || |  | | |  |     |  |  | ||  |||   ||||||     |||| ||| ||         |  |||| | || |||||| |||| || |||||||| ||||| || || |||||||||||||| |||||||| 
------------------------------gtacgtatgctttt---ccatttcttgtttggct--tagagtt-----taaactttgtgg------aaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT
                                   ttttgat  putative branch site (score: 4)
                             taaagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA