RetrogeneDB ID: retro_cpor_1417

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:35989826..35990217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN4
• Ensembl ID: ENSCPOG00000012478
• Aliases: None
• Description: None

Sequence

>retro_cpor_1417
ACCATGAACAAGGCGGCAGCAGAAGACCTCAATGTTACTGTCGAAGAGCAACAGAAGATAAACAGATTTGCGCAGGACAC
GAGTAGAACCACAGAGCTAAAGGAAGAAATAGAAGTAAAAAAGAAGCAACTCCAGAATCTAGAAGATGCTTGTTACGACA
TCATGCTCTCAGATGACGATTGCTTAATGATACCTTATATCGGCGATGTTTTCCAATAGCCATTCTCAAGAAGAAACACA
AGAAATGGTATAAGAAACAAAGAAAAATTTACAAGAAGGAATTGATGCCTTAGAATCCAGAGTAGCATCAATTCAGCAGG
TGCTAGCAAATTTGAAAGTTCAATTATATGTGAAATTTGCCAGCAACAGAAACCTTGAAGCTGATGAAAGT

Alignment

ORF - retro_cpor_1417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.06 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVYRQAAEDVNVTFEDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACDDIMLADDDCLMIPYQIGD
          T....AAED.NVT.E.QQKIN.FA..TSR.TELKEEIEVKKKQLQNLEDAC.DIML.DDDCLMIPY.IGD
Retrocopy TMNKAAAEDLNVTVEEQQKINRFAQDTSRTTELKEEIEVKKKQLQNLEDACYDIMLSDDDCLMIPY-IGD

Parental  VF-ISHSQEETQEMLEEAKKNLQEEIDALESRVASIQRVLADLKVQLYAKFGSNINLEADES
          VF..SHSQEETQEM..E.KKNLQE.IDALESRVASIQ.VLA.LKVQLY.KF.SN.NLEADES
Retrocopy VF>NSHSQEETQEMV*ETKKNLQEGIDALESRVASIQQVLANLKVQLYVKFASNRNLEADES

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	4.89 RPM
SRP017611_kidney	0.00 RPM	4.71 RPM
SRP017611_liver	0.00 RPM	4.61 RPM
SRP040447_lung	0.00 RPM	4.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.85 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1417 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1417 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 24 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013164	2 retrocopies	retro_amel_1313, retro_amel_1469,
Bos taurus	ENSBTAG00000008812	1 retrocopy	retro_btau_585,
Canis familiaris	ENSCAFG00000011856	1 retrocopy	retro_cfam_60,
Callithrix jacchus	ENSCJAG00000002615	3 retrocopies	retro_cjac_1996, retro_cjac_2869, retro_cjac_4114,
Cavia porcellus	ENSCPOG00000012478	3 retrocopies	retro_cpor_1417 , retro_cpor_1428, retro_cpor_598,
Erinaceus europaeus	ENSEEUG00000002733	1 retrocopy	retro_eeur_597,
Felis catus	ENSFCAG00000013355	2 retrocopies	retro_fcat_1031, retro_fcat_219,
Homo sapiens	ENSG00000101132	2 retrocopies	retro_hsap_3693, retro_hsap_4748,
Gorilla gorilla	ENSGGOG00000027337	2 retrocopies	retro_ggor_2497, retro_ggor_2950,
Myotis lucifugus	ENSMLUG00000008582	3 retrocopies	retro_mluc_1343, retro_mluc_510, retro_mluc_940,
Macaca mulatta	ENSMMUG00000017300	2 retrocopies	retro_mmul_1603, retro_mmul_2530,
Mustela putorius furo	ENSMPUG00000006173	2 retrocopies	retro_mputfur_664, retro_mputfur_791,
Mus musculus	ENSMUSG00000052033	1 retrocopy	retro_mmus_2763,
Nomascus leucogenys	ENSNLEG00000007023	2 retrocopies	retro_nleu_1247, retro_nleu_2548,
Oryctolagus cuniculus	ENSOCUG00000004940	5 retrocopies	retro_ocun_1210, retro_ocun_1432, retro_ocun_1525, retro_ocun_287, retro_ocun_344,
Otolemur garnettii	ENSOGAG00000016375	1 retrocopy	retro_ogar_2411,
Ochotona princeps	ENSOPRG00000005385	5 retrocopies	retro_opri_1006, retro_opri_211, retro_opri_396, retro_opri_425, retro_opri_866,
Oryzias latipes	ENSORLG00000019179	1 retrocopy	retro_olat_25,
Pongo abelii	ENSPPYG00000025840	1 retrocopy	retro_pabe_187,
Pan troglodytes	ENSPTRG00000013641	2 retrocopies	retro_ptro_2504, retro_ptro_3161,
Sus scrofa	ENSSSCG00000007487	2 retrocopies	retro_sscr_1009, retro_sscr_787,
Ictidomys tridecemlineatus	ENSSTOG00000028253	1 retrocopy	retro_itri_1565,
Tarsius syrichta	ENSTSYG00000008974	4 retrocopies	retro_tsyr_1040, retro_tsyr_1667, retro_tsyr_281, retro_tsyr_702,
Tursiops truncatus	ENSTTRG00000003850	3 retrocopies	retro_ttru_103, retro_ttru_861, retro_ttru_898,