RetrogeneDB ID: retro_cpor_934

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:3857276..3857698(-)
• Located in intron of: ENSCPOG00000011562

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCDC90A
• Ensembl ID: ENSCPOG00000014899
• Aliases: None
• Description: None

Sequence

>retro_cpor_934
AAGCTAAGCTTATCTGCACAGTACCTGCAGCTGTAGCATAAAAGGACAGATTTCATCTCTCTCAGGAATCAGACGCTCTA
CTTCAACACTCATGCCTTAGTATGTTTAGTGGAAAAAAATGGATTTACAACTCAACAAGCAGAAAGCATTGTGTCTGTCT
TGTTCAAGATCATGGAGGCCATCGTCTACAAAAACATGATCACCAAGGTGTAGCAAGAGATGTCTCTTCAGTAAACAATG
TCTAAGATTGCAAATATGAAAAAGGACACAATTATTTTGAAGAAGAGTAAATTTTAAGCCCTGAGAGCAGAAAATGAGAA
AAAAGAGCTTAAACTTCATCAGTTAAAACAAAAGAAATGGATGAAGTGATCAAAGTCTGAACAGATACCAAGTTAGAATT
CAATCTAGAAAAAAGCAGAGTA

Alignment

ORF - retro_cpor_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELSLSAPCLQLEHRRTGFTSPGHQKLYFDTHALVCLLEANGFTTQQAEIIASALVKIMEANVDIVYKDMV
          .LSLSA..LQL.H.RT.F.S...Q.LYF.THALVCL.E.NGFTTQQAE.I.S.L.KIMEA...IVYK.M.
Retrocopy KLSLSAQYLQL*HKRTDFISLRNQTLYFNTHALVCLVEKNGFTTQQAESIVSVLFKIMEA---IVYKNMI

Parental  TKVQQEITLQQIMSKISNVKKDMIILEKSEFSALRAENEKIKLELHQLKQ-QVTDEVIKVRTDTKLDFNL
          TKV.QE..LQ..MSKI.N.KKD.IIL.KS.F.ALRAENEK..L.LHQLKQ....DEVIKV.TDTKL.FNL
Retrocopy TKV*QEMSLQ*TMSKIANMKKDTIILKKSKF*ALRAENEKKELKLHQLKQ<KEMDEVIKV*TDTKLEFNL

Parental  EKSRV
          EKSRV
Retrocopy EKSRV

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	16.45 RPM
SRP017611_kidney	0.00 RPM	61.14 RPM
SRP017611_liver	0.00 RPM	4.22 RPM
SRP040447_lung	0.00 RPM	11.40 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_934 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_934 was not experimentally validated.

Homology

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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934 ,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,