RetrogeneDB ID: retro_cpor_361

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_132:2799599..2800205(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSCPOG00000012101
• Aliases: None
• Description: None

Sequence

>retro_cpor_361
GAAGAAGAAATTACTGCTTTTGTCATTGACAATGGCCCTGGATGTGCAAGTGGATTTGCTGGAGATGCACCCTCCCCAGC
TGTATTGCTTTCTATCACTGGCTCCCCTGATACCAGGGCATGATGGTGTGCATGGGTCAGGAGGATTCCTATGTGGGCAA
CGAGGCCCAGAGAAAGTGCAGAATCCTGAGTTTTAAGTACCTCATCGAGCATAGCATTGTCACCAACTGGGATGACATAG
AGAGGATCTCAGGCTACACTTACACTGAGCTGTATGTGATCCCTCAGGAGCACCTAGTGCTGCTGGTGGAGGCCACCCTG
AAGCCCAAAAACCAACATAGAGATGACTCAGATCATGTTTGAGGCCTTTAACAGCCAGGCCATGTATGTGGCCATTCAGC
CCATGCTGTCCCTATTTACCTCTTGACGCACTACTGACATTGTCATGGACCTTGGCAGTGGATTTACTCACATGGTGCCT
ATCTATGAGAGCTATGCCCTCTCCCACGCCATCCTTTGTCTGGACCTGGCCAACTAAGACCCAGTAGACTACCTCATCAA
GATCCTGATGGAATGTGACTAAAGCTTCACCACATGCCCAAGCAGA

Alignment

ORF - retro_cpor_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.77 %
• Parental protein coverage: 54.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPR-HQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          EEEI.A.VIDNG.G.C..GFAGD....AV..SI.G.P...QG.MV.MGQ.DSYVG.EAQ.K..IL..KY.
Retrocopy EEEITAFVIDNGPG-CASGFAGDAPSPAVLLSITGSPD<YQGMMVCMGQEDSYVGNEAQRKCRILSFKYL

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREK-MTQIMFETFNTPAMYVAIQAV
          IEH.IVTNWDD.E.I...T.Y.EL.V.P.EH.VLL.EA.L.PK.N....MTQIMFE.FN..AMYVAIQ..
Retrocopy IEHSIVTNWDDIERISGYT-YTELYVIPQEHLVLLVEATLKPK-NQHR>MTQIMFEAFNSQAMYVAIQPM

Parental  LSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAER
          LSL..S.RTT.IVMD.G.G.TH.VPIYE.YAL.HAIL.LDLA..D..DYL.KIL.E...SFTT...R
Retrocopy LSLFTS*RTTDIVMDLGSGFTHMVPIYESYALSHAILCLDLAN*DPVDYLIKILMECD*SFTTCPSR

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	0.23 RPM	468.99 RPM
SRP017611_kidney	0.00 RPM	445.13 RPM
SRP017611_liver	0.30 RPM	341.21 RPM
SRP040447_lung	0.20 RPM	1383.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	357.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_361 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_361 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 22 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361 ,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,