RetrogeneDB ID:

retro_sara_234

Retrocopy
location
Organism:Shrew (Sorex araneus)
Coordinates:scaffold_118197:448..712(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VAMP4
Ensembl ID:ENSSARG00000001709
Aliases:None
Description:vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645]


Retrocopy-Parental alignment summary:






>retro_sara_234
ATGCCTCCCAAGTTCAAGCGCCACCTGAATGATGACGACATCACTGCATCCGTGAAGAGTGAAAGGAGGAATCTTCTCGA
AGATGACTCAGACGAAGAAGAGGACTTTCTCCTGAGGGGGCCTTCCAGACCAAGATTTGAACCCAGGAATGATAAGATCA
GCATGTTCAGAATCAGGTGGACGAAGTCATCGATGTCACGCCAGAAAATTCACGAAGGTCATCGAAAGGGGGAGAGAGTA
GAAGAACTCCAGGACAAATCAGAT

ORF - retro_sara_234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.61 %
Parental protein coverage: 62.86 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMPPKFKRH-NDDDVTGSVKSERRNLLEDDSDEEEDFFLRGPSGPRFGPRNDKI-KHVQNQVDEVIDVMQE
MPPKFKRH.NDDD.T.SVKSERRNLLEDDSDEEEDF.LRGPS.PRF.PRNDKI..HVQNQVDEVIDV..E
RetrocopyMPPKFKRHLNDDDITASVKSERRNLLEDDSDEEEDFLLRGPSRPRFEPRNDKI<QHVQNQVDEVIDVTPE
ParentalN-ITKVIER-GERLDELQDKSE
N..TKVIER.GER..ELQDKS.
RetrocopyN<FTKVIER<GERVEELQDKSD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Sorex araneus was not studied using RNA-Seq expression data.
Sorex araneus was not studied using ChIP-Seq data.
Sorex araneus was not studied using EST data.
Sorex araneus was not studied using FANTOM5 data.
retro_sara_234 was not experimentally validated.

Retrocopy orthology:
Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 7 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000001244 retrocopies
Macropus eugenii ENSMEUG0000001122613 retrocopies
Monodelphis domestica ENSMODG000000038111 retrocopy
Otolemur garnettii ENSOGAG000000267451 retrocopy
Sorex araneus ENSSARG00000001709 2 retrocopies
retro_sara_234 , retro_sara_79,
Sarcophilus harrisii ENSSHAG000000171792 retrocopies
Tupaia belangeri ENSTBEG000000108292 retrocopies



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