RetrogeneDB ID: retro_cpor_777

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:17785659..17785973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSCPOG00000007310
• Aliases: None
• Description: None

Sequence

>retro_cpor_777
GTCACAGTCTTTTCTCTACTGGACTGCTGTGAGTTAATCTTCCTCTCCATGTACTTCATCATTACATTGTCTGATTTAGA
TGTGATTATATTAATGCTAAATCATGTTGCTCAAAATTAAACAAGCAGGTAATTCCAGAAATGATCGGCCATTGGATTGT
CAGCATATGGATGCTTGCTTACTGCAGTGGCAGCTGCCTTCTCAACTGACCTGTTGCCACGTGGAATATATATAGGTTCA
TTACGGTGCCAAGTGGCAACATGGGAGTGTTCGACCCAACAGAAACACACAATCAAGGGCAGAGAAGAAGCCAT

Alignment

ORF - retro_cpor_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 76.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFVFSLLDCCALIFLSVYFIITLSDLE-CDYINARSCCSKLNKWVIPEMIGHSIVSVLMLVSLHWFIFLL
          V.VFSLLDCC.LIFLS.YFIITLSDL..CDYINA.SCCSKLNK.VIPEMIGH.IVS..ML........L.
Retrocopy VTVFSLLDCCELIFLSMYFIITLSDLD<CDYINAKSCCSKLNKQVIPEMIGHWIVSIWMLAYCSGSCLL-

Parental  NLPVATWNIYRFIMVPSGNMGVFDPTEIHNRGQLKSH
          N.PVATWNIYRFI.VPSGNMGVFDPTE.HN.GQ..SH
Retrocopy N*PVATWNIYRFITVPSGNMGVFDPTETHNQGQRRSH

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	4.54 RPM
SRP017611_kidney	0.21 RPM	11.72 RPM
SRP017611_liver	0.04 RPM	14.49 RPM
SRP040447_lung	0.10 RPM	13.67 RPM
SRP040447_skeletal_muscle	0.01 RPM	9.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_777 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_777 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777 ,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,