Was this page helpful?

PseudoGene & ncRNA

    Table of contents
    No headers

    1. Probable ncRNA: 70451-71400

    This region was predicted by GeneMark as a gene, but Blastx and Blastp cannot find any matchable protein across all plants. Interestingly, when we ran a Blastn using EST database we observed good hits in 70460-70857, 70882-70953, and 71034-71181 with Zea mays. We assume this region as a potential ncRNA or microRNA coding candidate.

    G7_EST.bmp

     

    2. Pseudogene for protein phosphatase type 2C [Zea mays]: 145753-146310

    This is the 9th gene predicted by GeneMark in masked reverse strand. However, when we ran Blastp with the protein sequence, it only covered about half of the protein "phosphatase type 2C" in Zea mays, although with 100% query coverage and e-value 5e-29.  

    G9.bmp

    GENE ID: 100284674 LOC100284674 | catalytic/ protein phosphatase type 2C [Zea mays] (10 or fewer PubMed links)

    Score = 113 bits (282), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 76/160 (48%), Positives = 90/160 (56%), Gaps = 14/160 (9%) 

    Query  1    EALALVSLIDD-EKKFGDCQFDLWKQYYVVACVAVFGKLRRNRRLDAVQSGCTALSISNK  59

                EALAL SLIDD +KK GDCQFDLWK+ YV AC AV  +LRR+RRLDAVQSGCTALSI  +

    Sbjct  118  EALALASLIDDGKKKLGDCQFDLWKRSYVAACAAVDDELRRSRRLDAVQSGCTALSIVKQ  177

    Query  60   G----TSWSSPTPVTLGLFWAPHPTTAPSHRPAHHHWKLNLPHKS----LLTGHEFSCAR  111

                G     +    +   LG  +      A          K NLP +        G  +  A

    Sbjct  178  GDLMVVANVGDSRAVLGTTYGDGTIVAVQ---LTVDLKPNLPQEKERIRRCNGQVYCLAD  234

    Query  112  TTVVADI--PNQESSVLAMSCAFDDYYIKDYGVILAPEVT  149

                   V  +  P++ES  LAMS AF DY +KD GVI  PEVT

    Sbjct  235  EPGVHRVWQPSRESPGLAMSRAFGDYCVKDCGVISTPEVT  274

    The real protein phosphatase type 2C [Zea mays] should have 351 aa.

    Was this page helpful?
    Tag page (Edit tags)
    • No tags

    Files 2

    FileSizeDateAttached by 
     G7_EST.bmp
    No description
    960.05 kB14:15, 29 Nov 2012cui19Actions
     G9.bmp
    No description
    960.05 kB00:06, 30 Nov 2012cui19Actions
    You must login to post a comment.