RetrogeneDB ID: retro_cpor_205

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:28673558..28674384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSCPOG00000007677
• Aliases: None
• Description: None

Sequence

>retro_cpor_205
ATGGCGGATCTGGAGGTGCAGTTGTGTGATGAAGAGAAGCAGCGACAGCAGCAAAATTCATCATTCATGTCCCTCCTGGA
GAGTTTAATGAGGTTTTTTAATGATGTTCGGTTATTGCTTAATAATGATAATGTCCTCAGGAAAGGAGCAGCCCATGCAT
TTGCACAGTATAGCTTGGATCAGTTTACTCCAGTAAAAATTGAAGGTTTTGAAGATCAGGTATTGATTACAGAACATGGT
GATTTGGGAAATGGAAAGTTTTTGGATCCAAAAAACAGAATTTGTTTCAAATTTGATTGCTTAAGAAAGGAAGCAATTGA
TCCAAGACCTACAAAGCAGAAAATGCAATTGAATCATGGAGAGCTTCTGTAGGAACTGCGCTGTGAGCATACGTAAAAGA
ACATTACCCGAATGAAGTTTGTATTGTGTATGGTAAAAAAATAGATGGACAGCAAACCATTATTGCATGCATAGAAAGCC
ATCAATTCCAAGCAAAAATTTTTTTGAATGATTGTTGGAGGTCAGAGTAGAAGTTTACAATCACACCTTCAACCTCTCAG
GTGGTTGGCATCTTGAAAACTCAGGTTCATTATTATGAAGATGGTAATGTTCAGCTAGTGAGTCATAAAGATCTACAAGA
TTCCCTAACAGTGTCTAATGAAGTGCAAACAGCAAAAGAATTTATAAAGATTGTAGAAGCTTCAGAAAATGAATACCAGA
CTGCCATCAGTGAGAATTATCAGACAATGTCGGACACTACTTTCAAAGCCTTACATTGACAGTTGCCATTACACGTACTA
AGATTGATTGGAACAAGATCCTTAGC

Alignment

ORF - retro_cpor_205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADLEEQLSDEEKVR-IAAKFIIHAPPGEFNEVF-NDVRLLLNNDNLLREGAAHAFAQYNLDQFTPVKIE
          MADLE.QL.DEEK.R..AAKFIIH.PPGEFNEVF.NDVRLLLNNDN.LR.GAAHAFAQY.LDQFTPVKIE
Retrocopy MADLEVQLCDEEKQR<TAAKFIIHVPPGEFNEVF>NDVRLLLNNDNVLRKGAAHAFAQYSLDQFTPVKIE

Parental  GYEDQVLITEHGDLGNGKFLDPKNRICFKFDHLRKEATDPRP-YEAENAIESWRTSVETALRAYVKEHYP
          G.EDQVLITEHGDLGNGKFLDPKNRICFKFD.LRKEA.DPRP.Y.AENAIESWR.SV.TAL.AYVKEHYP
Retrocopy GFEDQVLITEHGDLGNGKFLDPKNRICFKFDCLRKEAIDPRP<YKAENAIESWRASVGTAL*AYVKEHYP

Parental  NGVCTVYGKKIDGQQTIIACIESHQFQAKNFWNGRWRSEWKFTITPSTTQVVGILKIQVHYYEDGNVQLV
          N.VC.VYGKKIDGQQTIIACIESHQFQAK.F.N..WRSE.KFTITPST.QVVGILK.QVHYYEDGNVQLV
Retrocopy NEVCIVYGKKIDGQQTIIACIESHQFQAKIFLNDCWRSE*KFTITPSTSQVVGILKTQVHYYEDGNVQLV

Parental  SHKDILDSLTVSNEAQTAKEFIKIVEAAENEYQTAISENYQTMSDTTFKALRRQLP-VTRTKIDWNKILS
          SHKD..DSLTVSNE.QTAKEFIKIVEA.ENEYQTAISENYQTMSDTTFKAL..QLP..TRTKIDWNKILS
Retrocopy SHKDLQDSLTVSNEVQTAKEFIKIVEASENEYQTAISENYQTMSDTTFKALH*QLP<ITRTKIDWNKILS

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	4.89 RPM	52.97 RPM
SRP017611_kidney	3.77 RPM	41.56 RPM
SRP017611_liver	3.61 RPM	39.74 RPM
SRP040447_lung	1.41 RPM	46.23 RPM
SRP040447_skeletal_muscle	2.69 RPM	79.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_205 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_205 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.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205 ,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,