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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttgagcttaatttgtgggtgtgtgatacacactcagctcgggttgttgtggacttcactttggatttcatttagggtttggcttttgcagaca...

Basic information

species Physcomitrella patens
transcript PP1S371_31V6.2
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S371_31V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 3
CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttgagcttaatttgtgggtgtgtg-atacacactc-----agctcgggttgttgtggacttcactttggatttcatt-tagggtttggcttttgcagaca----
  || |||||||||||  | || |||||| |  | |||| |||||||||||||||||||||||| || |||||||| ||||||||| | || |||||||||  | |   | | |     | |  || ||    |     |  || |||| || |  |||  |  || | | | ||  ||  || || |||      |||    
AGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTTGTGAGATTTgtatcctttttgttctttgtatcatgatatttatgcatttcctcgtaaattctggttattat--actatatatttgttattatcatactgtatgccttaatagtacattag

upper sequence: PP1S371_31V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 3
CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttgagcttaatttgtgggtgtgtg-atacacactc-----agctcgggttgttgtggacttcactttggatttcatt-tagggtttggcttttgcagaca----
  || |||||||||||  | || |||||| |  | |||| |||||||||||||||||||||||| || |||||||| ||||||||| | || ||||||||| || |   ||| |    || |  || ||    |     |  || ||||||| |  ||   |  ||   | | ||  ||  || || |||      |||    
AGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTTgtgagatttgtatccttttagttctttttatcatggtatttatgcatttcctcgtaaattctggttgttat--accatatctttattattatcatactgtatgccttaatagtacattag

upper sequence: PP1S371_31V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 3
CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttgagcttaatttgtgggtgtgtgatacacactcagctcgggttgttgtggacttcac---tttggatttcatttagggtttggcttttgcagaca
| || ||||| |||||  | || |||||  |  |||  | |||||| || |||||||||||||| ||||| ||| | || |||||||| || |||||||||||   | |||||    | ||   |  ||     |||  |||  || ||  || ||      |  |||  || |      | | | ||       
CTGGCAAGACAGACTACAGGGCCAGGATAAGGCTGATTAACCAAGACAAAAACAAGTACAACACACCCAAATACAGATTTGTTGTGCGATTTgtatcctttga---ttatttgaccatctggtttctacctattgctatggtactt-tgagctccagaagcatatattgtatctcttaactagatattcttag--

upper sequence: PP1S371_31V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 4
CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcct----ttgagcttaatttgtgggtgtgtg-atacacactcagct-cgggttgttgtggacttcactttggatttcatttagggtttggcttttgcagaca
| || ||||| ||||||||||| ||||||||| ||| ||  ||||| ||||| ||||||||||| || || || || || || ||||| || |||||||    |  || || |||      | | ||  |    |||      |    || | || | || |  | |||    |   ||   ||   |  |  |    
CGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTTgtatcctaatatcaagtttgattctactttttatgcgtgtgtactggttggccctctggtatgtaattaagatgggag---acacagaaatttattacttaaa---

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|208382974|gb|DC927724.1|DC927724
EST:     AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTC                         ACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
genomic: AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttg ... accctttcagACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
EST: gi|67577808|gb|BJ949975.1|BJ949975
EST:     AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTC                         ACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
genomic: AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttg ... accctttcagACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
EST: gi|208373862|gb|DC956336.1|DC956336
EST:     AAGTACCGTTTCGNTGTGCGGTTC                         ACCAACAAGGATATTGTTGCGCAANTCACCTATGCCACTCTTGCTGGAGAT
genomic: AAGTACCGTTTCGTTGTGCGGTTCgtatcctttg ... accctttcagACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
EST: gi|67508343|gb|BJ941211.1|BJ941211
EST:     AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTC                         ACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
genomic: AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttg ... accctttcagACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
EST: gi|67573313|gb|BJ946137.1|BJ946137
EST:     AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTC                         ACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT
genomic: AAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttg ... accctttcagACCAACAAGGATATTGTTGCGCAAATCACCTATGCCACTCTTGCTGGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCgtatcctttgagcttaatttgtgggtgtgtgatacacactcagctcgggttgttgtggacttcactttggatttcatttagggtttggcttttgcagaca

- - - - - - - - - - - - - - - - - - - - - - -  AAGAAC