RetrogeneDB ID:

retro_cpor_947

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_36:10951108..10951548(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000019941
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_947
AAGATCTGCCTAGGATACAGGAGGAGTTATACGCCAGTACCAACTGAAGGTTTTCCAGTTTCTTAATACAAAAATCAAAT
CTGCATTCCTTTCCACGAAGTATCCTCAATAGATAAACCGGATTGTCCTTTACAGAAGAAAGCACAAAATGGAGCAGTCG
AAAGAAATTCAAAAGAAAAGAACATGGCAAGCAGTCAAATTGCAGGCCATCACTGGTGCATCTCTTGCTGATAAAAATAA
TAGCCAAGAGGAATCAGAAACCAGAAGTTACAAAGGCCTAAAGAGAACAAGCTATCAGGGCTGCCAAGGGAAGCGGAAAA
AAGGTTAAGTAAGCATCTAAAAAGACTGCAATGGCTGCTGCAGAGGCTCCCACAAAGTCAATACCCAAACAGAAGATTGT
GAAGCCTGTAAAAATTTCTGTTACCCGAGCTGATGGAAAA

ORF - retro_cpor_947 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.19 %
Parental protein coverage: 92.36 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKIYPGHGRRYARTDG-KVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVKFQR
KI..G..R.Y......KVFQFLN.K..SAFLS...P..IN..VLYRRKHK..QS.EIQKKRT..AVK.Q.
RetrocopyKICLGYRRSYTPVPT>KVFQFLNTKIKSAFLSTKYPQ*INRIVLYRRKHKMEQSKEIQKKRTWQAVKLQA
Parental-AITGASLADIMAKRNQKPEVRKAQREQAIRAAK-EAKKAKQASKKTAMAAAKAPTKAAPKQKIVKPVKV
.......L..I.AKRNQKPEV.KA.REQAIRAAK...KK.K.ASKKTAMAAA.APTK..PKQKIVKPVK.
Retrocopy>SLVHLLLIKIIAKRNQKPEVTKA*REQAIRAAKGSGKKVK*ASKKTAMAAAEAPTKSIPKQKIVKPVKI
ParentalSAPRVGGK
S..R..GK
RetrocopySVTRADGK

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 92 .08 RPM
SRP017611_kidney 0 .00 RPM 147 .09 RPM
SRP017611_liver 0 .00 RPM 119 .31 RPM
SRP040447_lung 0 .03 RPM 162 .90 RPM
SRP040447_skeletal_muscle 0 .00 RPM 192 .59 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_947 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_947 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 33 parental genes, and 191 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037403 retrocopies
Bos taurus ENSBTAG000000134611 retrocopy
Canis familiaris ENSCAFG000000096014 retrocopies
Callithrix jacchus ENSCJAG000000004963 retrocopies
Cavia porcellus ENSCPOG00000019941 5 retrocopies
Dasypus novemcinctus ENSDNOG000000031949 retrocopies
Equus caballus ENSECAG000000240951 retrocopy
Erinaceus europaeus ENSEEUG000000093203 retrocopies
Felis catus ENSFCAG000000033271 retrocopy
Homo sapiens ENSG000001143918 retrocopies
Gorilla gorilla ENSGGOG000000116098 retrocopies
Loxodonta africana ENSLAFG000000138043 retrocopies
Macropus eugenii ENSMEUG000000091777 retrocopies
Myotis lucifugus ENSMLUG000000170054 retrocopies
Macaca mulatta ENSMMUG000000150599 retrocopies
Monodelphis domestica ENSMODG000000019163 retrocopies
Mustela putorius furoENSMPUG000000117383 retrocopies
Nomascus leucogenys ENSNLEG000000032766 retrocopies
Oryctolagus cuniculus ENSOCUG000000007918 retrocopies
Otolemur garnettii ENSOGAG000000138438 retrocopies
Ochotona princeps ENSOPRG000000042556 retrocopies
Procavia capensis ENSPCAG000000059181 retrocopy
Pongo abelii ENSPPYG000000135886 retrocopies
Pan troglodytes ENSPTRG000000151762 retrocopies
Pteropus vampyrus ENSPVAG000000098893 retrocopies
Rattus norvegicus ENSRNOG0000000161125 retrocopies
Sorex araneus ENSSARG000000076156 retrocopies
Sarcophilus harrisii ENSSHAG000000082262 retrocopies
Sus scrofa ENSSSCG000000119524 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000146542 retrocopies
Tupaia belangeri ENSTBEG0000001204430 retrocopies
Tarsius syrichta ENSTSYG000000023144 retrocopies
Vicugna pacos ENSVPAG000000122463 retrocopies



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