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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA

Basic information

species Physcomitrella patens
transcript PP1S10_254V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
tcatgtattttctgtagtaccaaggtgttcc-ttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttatta--ttgc-agGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
  ||  | |      | ||      | || | |||  | |||||    |   | | | ||   |  ||   |  || | ||||   | |  || |  |||| ||||||   || | || |  || || |  || || || || ||||| || ||||||||||| || || |||||||||||||| || || |||||||||||||
ctatcaaatactgaaattatgtcattattgcatttaatttggac----caagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G388148_T01 (Zea mays), 3'ss of exon 3
--tcatgtattttctgtagtaccaaggtgttccttttttatggacatt--tcccctcaatctgggtcagtg-gatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
  | ||  || ||   | || | |     ||||      ||  ||  |  |  | |   |   | |   || ||   | | |||| | ||    | |   |  ||||  || ||||||     ||  | |  |  || ||| | ||||| |||||||||||||| || || ||||| |||||||| || ||||||| |||||| |
cttaatccatatttgtttgtgctat----ttcccaaccaatacactctagtttctttgcttgagctgcatgtgaccactgcactacttgactaatgtctat-tagGATAATTCTGGAGCAGTCCCTCTCGTAGCAAAGCACCATAAAGGTTGTCATTGCAAGAAGTCAGGATGCCTAAAGAAGTACTGTGAATGCTACCAAGCAA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaacttt--attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
  ||  |||    | | ||      | || | |||   |       |    |    |||  |       |  |   | |  |||  | |   ||| |  |||||||   || | || |  || || |  || || || || ||||| || ||||||||||| || || || ||||||||||| || || |||||||||||||
--atcaattacaggcattatatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
-----------------------------------tcatgtattttctgta--gtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagt---ggatttcgg--aactaataga--actttattattgcagGAGGATGCTGGAGAGCA----TCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA------
                                   | ||   ||||  | |   | |      ||    |||||   ||   | |       |||||||   |     ||||  |  ||||  | |   | || | |||       | |  | |||  |      || | |    || || ||||| ||||||||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| |      
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
----------------------------tcatgtatt----ttctgtagtaccaaggtgtt---ccttttttatg-gacatttcccctcaatctgggtc-agtggatttcggaactaata---gaactttattattgcagGAGGATGCTGGA----GAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA------
                             ||||| ||     | | | | |  | | | ||   ||   ||| || ||   | |       |||||||  ||  ||| | | |  |||     | | || | |||       | |  | |||    ||   |  | |    || || ||||| ||||||||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| |      
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
tcatgtatt----ttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaacttt----attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
  ||||  |    ||    |        || ||   | ||||   | || |    |   ||| | |   ||  | | |  |||| |  ||||||    || | || ||||||| ||||| ||   |  | |    || ||||| ||||| || |||||||| || ||||| ||||||||||||||||| || |||||||||||||| |
--atgtgctgaacttgaacatcttttttgtattttatatttaaaaa-atctttagtttttctagttt--tgagtcttg--acta-tctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 2
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaa---tagaacttt----attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
      |  |  || ||    ||  | ||  |||||| || || |      ||  |  |  |   | |  ||  |   | |   | |||||||    || | || ||||||||||||| ||   |  | |    || ||||| ||||| || |||||||| || || || |||||||||||||||||||| |||||||||||||| |
------aagtgttg-agcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
----------tcatgtattttctgtagtacc----aaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
          ||| ||| ||| | ||||||     ||| |||| | ||||| |     || |   | |||   | | | |  || |  |||||  |  ||    || | || ||||||||||||| ||   |    |   ||| || || || ||||| || ||||| || ||||| |||||||||||||||||||| || ||||||||||| |
ttttctgaactca-gtaatttttctagtactggtaaagatgttgcattttttt---tcttactttttaatt--gttgact--atctgtgaact--tcaaa----ataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
          | ||| ||      |||||    | || |  ||  ||   || ||  | | |   |   ||    |  |      |||  |||  |||||||||| | ||| ||   |    ||   |  | |||||||||||| ||||| |||||||||||||| || || ||||||||||| || ||||| ||||| |
---------gtatgtggttt----gtgttatgctctt-taaactgttggtcttaaggttgttggataagttataaattttg----actcgatt--tgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
          |  || || |  |||   |  || |  || |                  | ||  |    |||  |  || |     |||    ||| ||||||||   || ||   |   |||   || ||||| ||||||||||| || ||||| ||||| || ||||| |||||||||||||| ||||| ||||| |
---------gtacgtggtcctgaggaacttgttctagatcg-----------tgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA

upper sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
---tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
      |   ||  ||  ||     |  |  ||  |||| ||| | |||        || |   |   |   ||  ||    ||  |  |   |  | |  |||| || |||||  |    ||||||| ||| || ||||| |||||||| || ||||||||||| || |||||||||||||| || || ||||| ||||| |
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttct---ttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA

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: 29 (upstream exon), 23 (downstream exon)
Score: 2

TGAAACCGTGCGTCAGGAAGCGGTAGAAGCCACCTTAGAGCGAAATCCTAATGCATTTCGACCTAAGATATTTAGCAGTCCTGGTATGCGAGACTTGAGGgtacgttggc ... attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
                              aactaat  putative branch site (score: 2)
                                         ctttatt  putative PPT
                              aactaatagaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT