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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC

Basic information

species Physcomitrella patens
transcript PP1S277_14V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 2
tcatcgatgagaggcagaagggccggattgtagtct---ctgcagctacatgtgct---ccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
          |||     || ||||  |||    |     ||  | |||  | |     |    | |       |||    ||    ||  |    | | || ||||||||| ||||||||  | ||||| || ||||| ||||||||||| || || |||||||||||||| ||| ||||||||||||| ||  |   |||||||
-----cgcatgagctgatagtgccgttttggctaccgaaatgttgttacgagagtctgacaacacgatcccaatgtttgcacatggatttgtgaattgtgat-cagGTGGTCCCAGATTGCGGCGCAGCTGCCCGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACTCGTGCCTCAAGAAGAAGCTCCGGCAGCGCGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
-----------------------------------------tcatcg-atgagaggcagaagggccggattgtagtctctgcagct-acatgtgctccttgcaaatgttgagttaaagcagaatttgatc---ctgtat-aatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
                                         | |||  |  ||      ||   |     |  | |   |  ||||   |||   ||     || |  | | | |||   ||| || |||    || ||  |  ||||||||| ||||||||  | ||||| || || || |||||||||||  | || |||||||||||||||| ||||||||||||||| ||  |   |||||||
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
tcatcgatgagaggcagaagggccggattgtagtctctgcagct-acatgtgctccttgcaaatgttgagttaaagcagaatttgatc---ctgtat-aatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
      |  ||      ||   |     |  | |   |  ||||   |||   ||     || |  | | | |||   ||| || |||    || ||  |  ||||||||| ||||||||  | ||||| || || || |||||||||||  | || |||||||||||||||| ||||||||||||||| ||  |   |||||||
-----tactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g31470.1 (Oryza sativa), 3'ss of exon 2
-tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC-
 || | |   |   | |   | ||  |  | |  | |     |||   |  | |         || ||  |  |      |     ||| || |    ||||||| | ||||| || |  || || ||||| ||||||||||||||  | || || ||||||||||| ||||||||||||||||| | |  |   ||     
ttcttgggccatgcgtatg-gcgcatggctctgctttgctttgcttttttggattgaactggttggtgcatggagctcagaacgattcccgtgtgtctcagGTGGGCGCAGATCGCCAAGCACCTGCCAGGGCGCACGGACAACGAGGTGAAGAATTTCTGGAACTCGTGCATCAAGAAGAAGCT-CATCGCGCAGGGGCTC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
tcatcgatgagaggcagaagggccggattgtagtctctg-cagctacatgtgctc--cttgcaaatgttgagttaaagcagaatttgat-cctgta--taatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC-
      ||          | |   ||||  || |   || |||  |||| |  |   ||  |  |||   | |  |  |  | |  ||  | || |  || ||||||||||| ||||| ||  ||| |||||| || ||||| |||||||| || || ||||||||||||||   ||||||||||   || |   |  ||  | || 
-----catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctac-cgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCT-CAAGATCTCCTCCTCC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 3
----tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcaga--atttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
     | || ||   |    | |   ||  | |  ||     | | || || |    |  |   |    | |  |||  |||    | |  |  |  || | | |||||||| ||||||||| | ||||| || ||  | || |||||||| || || ||  ||||||| |||||||||||||||||||| ||  | |  ||||| 
gtaaacttcaatctcaattggcactaccaaaattcaggactagtaactgcaaggcaacactttgatacatcaactaacacagcccttctatttttccatga-gaagGTGGTCTCAGATTGCAGCTCAGCTGCCTGGGAGGACTGACAACGAGATCAAGAATCTCTGGAATTCTTGCATCAAGAAGAAGCTCCGGCAGAAAGGCATT

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G064744_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------tcatcgatgag--aggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgt-tgagttaaagca-gaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
                                                                                 | |||  | |   || || |     |  ||  |         |||| |  |    | |  ||      | |   | | || |   |||  ||||    || ||||||||| ||||| ||  | ||||| || ||  | ||||||||||| || ||||||||||||||||| ||||||||||||||||| ||  |    ||||||
gtaatttaactggtaatagcaagcaacagttaacacgcatgcatatggcatggcagcatgcagaggctgccacacttgtgctgatctgttacacagacaaacaatgccaataatctcactcagagctcctagcttacatgccagccacataacacacatcatgtgcttgtgcctgatccat-cagGTGGTCCCAGATCGCGTCGCAGCTGCCGGGGAGGACGGACAACGAGATCAAAAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCAGGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G147698_T01 (Zea mays), 3'ss of exon 2
tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgc-agGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
                          |   || | |       | ||||    | | || |    | |   | | | |||| ||| |   || |  || |||||||| ||||||||  ||||||| || ||||| |||||||||||  | || |||||||||||||| | ||||||||||| |||  |  |   |||||||
-----------------------gtaagcttaattttca----tgcatggatgcatggcgagcagtaatggagaac-gaatctgaacggttacatggccagGTGGTCTCAGATTGCGGCCCAGCTGCCTGGCCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCGTACATCAAGAAGAGGCTCAGGGAGCGCGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G172327_T01 (Zea mays), 3'ss of exon 2
-----------------------------------tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGG-CATC
                                   ||   | | |   |        | ||    | ||  |    ||  | | || ||  |||    |  | |   | ||  | |  |||||     |   ||| ||| | ||||| || |  || || || || |||||||| |||||  | || |||||||||||||| ||||||||||||||||| | |  |   || | ||
gtacgtacgggcatacttcttgccgtctatcttgctccctgctaactagtgactcaccggggccatggtgccat--gcctcgtctggtctgtgc----gcggcgcgcatgccaactccgatccaactca---cagATGGGCGCAGATCGCCAAGCACCTGCCCGGGCGCACGGATAACGAGGTCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCT-CATCGCGCAGGGCCTC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G003406_T01 (Zea mays), 3'ss of exon 2
--tcat-cgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
   | | | ||| |   | ||    ||   |  |   ||   |     ||   |      ||    |  |   | ||   | ||||  |   |     ||||||||||| ||||| ||  | ||  | || ||||| ||||||||||| || || ||||||||||||   ||| ||||||||||||||||| |   |||||||
gtacgtacaatgcgttccggaccaaccaactgatctccttacccagcgcagtgggcggcggcgcgcggcggcatcaat--gtatttcttttcgcg-ggtgcagGTGGTCGCAGATCGCGTCGCACTTGCCGGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGCGTCAGCGCGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G150841_T01 (Zea mays), 3'ss of exon 2
-----------------------------tcatcgatgagaggcagaagggccggattgtagtctctgc-agctacatg---tgctccttgcaaatgttgagttaaagcaga-atttgatcctgt-----------------ataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
                               |  |  ||    | |   |||| | || |  | | |   ||||   ||   || |  |    |||| |   |  || | |  || | || ||||                 || |  ||||||||| ||||||||  | ||||| || || || |||||||||||  | || |||||||||||||| | | ||||||||||||| ||  |   ||| |||
gtaggtggtgccacagtggcaggccatgcatacagcagatccccggcccggccagtttcttttatttattagctgtgtgcgatgatgatgatgaatgatccatccaatcggggatgtaattctgttcgttttgcacgtacgaatgacacagGTGGTCTCAGATTGCTTCGCAGCTGCCGGGGCGGACGGACAACGAGGTGAAGAACTTCTGGAACTCGTACGTCAAGAAGAAGCTCCGGCAGCGCGGGATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0005g02480.t01 (Vitis vinifera), 3'ss of exon 2
--------tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
        || ||  | |    |  ||   |   |   ||  || |     | | |||  | | || |  || |||  | |    |  ||||   ||   |    ||||||||| || || ||| | ||||| || || ||||| ||||| |||||||| || || |||||||||||| | |||||||||||  |  | |  ||||| 
gtcatcactcctctcttaatatctaaa---cttcaccttatcctttcttctttcttgtttttcatgta--tgctgacattactgggtttttggggcttcct----cagGTGGTCCCAAATCGCAGCACAGCTGCCTGGACGCACTGACAATGAAATAAAGAATTTGTGGAACTCTTGCTTGAAGAAGAAGCTCAGGCAGAGAGGCATT

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
tcatcgatgagaggcagaagggccggattgtagtctc-tgcagctacatgtgctcc---ttgcaaatgttgagttaaagc--agaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
              |   |   || |   | |  ||| | ||   ||      |     | | |  | |   |||  |      | |||  | |||| | || ||| ||||| ||||||||| | ||  |||| ||  | ||||| || ||||||||||| || |||||||| ||||| |||||||||||  |  | |  ||||||
-----------gtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagttttcctgttggattctgaagttttctgctgtttcat-cagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC

upper sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv13s0064g00960.t01 (Vitis vinifera), 3'ss of exon 1
tcatcgatgagaggcagaagggccg-gattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACA-TCGGCATC
   | | |   | ||| ||     | ||     |       |  | ||  |     | |   ||      |   |       ||  |     ||  | ||||||||| ||||| ||  | |  ||||||||  | || ||||| |||||||| |||||||||||||||  ||||||||| | ||||   ||||    |||  
-agtaggtcttaagcataattaatgtgaaaaatgaaaaaaaaaatgcagatttatttggttgattacacttctcattttccatttgtttcaaatggttcagGTGGTCTCAGATCGCGGCGCGCCTACCAGGGAGGACCGACAATGAAATAAAGAACTTCTGGAACTCTACCATCAAGAAAAGGCTGAAAAACAGCTTGCAG-

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: 35 (upstream exon), 23 (downstream exon)
Score: 3

TGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAGAGGAGAACTTGATCATTGACTTGCATGCTGTTCTTGGTAACAGgttctctcat ... tataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC
                                  atttgat  putative branch site (score: 3)
                                 aatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatcgatgagaggcagaagggccggattgtagtctctgcagctacatgtgctccttgcaaatgttgagttaaagcagaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC