RetrogeneDB ID: retro_sscr_787

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:136556415..136556791(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000006909
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFDN4
• Ensembl ID: ENSSSCG00000007487
• Aliases: None
• Description: Sus scrofa prefoldin subunit 4 (PFDN4), mRNA. [Source:RefSeq mRNA;Acc:NM_001123160]

Sequence

>retro_sscr_787
GCGGCCACCGTGAGGAAGGCGTGCTGCGGGAGATGTCACCGTTATTTCTGAGGATCAACCAAAGAGAAACACGTCTGCAC
AGAATCCAAGAAGAATCACAGAGCCGGCAGGAGAAATGGACGTCAAAAAGAAACAACTCCAAAATCCCGAGGATGCTTGT
GAGGACATTGTGCTTGCGGATGAGGGCTGCATAATGACACCTTATCAGATTGGTGATGTTGTCATTAGCCATTCTCAAGA
AGAAACTCAAGAAATGTTAGAAGAAGCACCAAAAAATCGGTCAGAAGAAACGGACGCCTTAGAATCCAAAGTGGGATCAA
TTCGGCCGGTGTTAGCAGATTTGAAAGTTCAGTTATATGCTAAATTTGGGAGGAAC

Alignment

ORF - retro_sscr_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 93.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AATMKKA-AAEDVNVTFEDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACEDIMLADDDCLMIPYQ
          AAT..KA.AA.DV.V..EDQ.K.N..A.N..RITE...E..VKKKQLQN.EDACEDI.LAD..C.M.PYQ
Retrocopy AATVRKA>AAGDVTVISEDQPKRNTSAQNPRRITEPAGEMDVKKKQLQNPEDACEDIVLADEGCIMTPYQ

Parental  IGDVFISHSQEETQEMLEEAKKNLQEEIDALESRVASIQRVLADLKVQLYAKFGSN
          IGDV.ISHSQEETQEMLEEA.KN..EE.DALES.V.SI..VLADLKVQLYAKFG.N
Retrocopy IGDVVISHSQEETQEMLEEAPKNRSEETDALESKVGSIRPVLADLKVQLYAKFGRN

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
SRP014902_placenta	0.00 RPM	1.33 RPM
SRP014902_testis	0.00 RPM	3.11 RPM
SRP018288_heart	0.00 RPM	16.48 RPM
SRP018288_kidney	0.00 RPM	6.40 RPM
SRP018288_liver	0.00 RPM	3.20 RPM
SRP018288_lung	0.00 RPM	7.54 RPM
SRP018856_adipose	0.00 RPM	2.67 RPM
SRP035408_brain	0.00 RPM	52.91 RPM
SRP035408_liver	0.00 RPM	14.12 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_787 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_787 has 0 orthologous retrocopies within eutheria group .

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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,