RetrogeneDB ID: retro_sscr_181

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:141418919..141419333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF4
• Ensembl ID: ENSSSCG00000008690
• Aliases: None
• Description: ring finger protein 4 [Source:HGNC Symbol;Acc:10067]

Sequence

>retro_sscr_181
ATGAACACAAAAATGTCCTATGGTACCAGGGTCAAGTCCAGATAGACATGAGAATTCCGTACAGCTGGGATAGGGAGCAC
AATTCCTGAGGTGATCTTGGAAGCAGAATTGTTAGAACTTGGAGAAAGTGATGAAATAGTTAACCTCACTTGTGAATCTC
TGGAGCCTGCAGTGATTGACCTAACTCACCATGAGTCCGTTGTGATTACTGAAGAAAGGAGGAGGTCAAGGGGAAACACA
TGTTTCCAAGGCCAAACTGGCAGCTGTGTGGGCAGTGATAAGGAGGGCTTGATGAGGGACAGAGATGTATATGTGACCAA
CAGTGCCTACCATAATGCCCTGGAAGAAAAAACTTTAAATGGCTCAGTACCTGGTTATATATGGTATTGAATTTGTAAGT
ATGGGTACTCAGAG

Alignment

ORF - retro_sscr_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.45 %
• Parental protein coverage: 74.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTRKRRGGAVNSRQA-QKRTRESPST-PEMALEAEPIELVESAGDEIVDLTCESLEPVVVDLTHNDSVV
          M.T....G..V.SR.....RT....ST.PE..LEAE..EL.ES..DEIV.LTCESLEP.V.DLTH..SVV
Retrocopy MNTKMSYGTRVKSR*T*EFRTAGIGSTIPEVILEAELLELGES--DEIVNLTCESLEPAVIDLTHHESVV

Parental  IVEERRRPRRNARRLRQDHADSCVVSSDDEELSRDRDVYVTTQTPRNAREEAATGLRPSGTVSCPICMDG
          I.EERRR.R.N.....Q....SC.V.SD.E.L.RDRDVYVT.....NA.EE........G.....IC..G
Retrocopy ITEERRRSRGNT--CFQGQTGSC-VGSDKEGLMRDRDVYVTNSAYHNALEEKTLNGSVPGYIWY*ICKYG

Parental  YSE
          YSE
Retrocopy YSE

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	48.71 RPM
SRP014902_testis	0.00 RPM	58.84 RPM
SRP018288_heart	0.00 RPM	23.42 RPM
SRP018288_kidney	0.00 RPM	53.09 RPM
SRP018288_liver	0.00 RPM	35.02 RPM
SRP018288_lung	0.00 RPM	66.19 RPM
SRP018856_adipose	0.00 RPM	76.11 RPM
SRP035408_brain	0.00 RPM	37.92 RPM
SRP035408_liver	0.00 RPM	30.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_181 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_181 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1144
Pongo abelii	retro_pabe_1240
Canis familiaris	retro_cfam_25
Equus caballus	retro_ecab_33

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Dipodomys ordii	ENSDORG00000006675	2 retrocopies	retro_dord_347, retro_dord_411,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Echinops telfairi	ENSETEG00000001683	3 retrocopies	retro_etel_469, retro_etel_626, retro_etel_627,
Felis catus	ENSFCAG00000004051	1 retrocopy	retro_fcat_897,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Myotis lucifugus	ENSMLUG00000005969	1 retrocopy	retro_mluc_1640,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Ochotona princeps	ENSOPRG00000004317	3 retrocopies	retro_opri_112, retro_opri_783, retro_opri_863,
Procavia capensis	ENSPCAG00000004528	1 retrocopy	retro_pcap_208,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Sus scrofa	ENSSSCG00000008690	1 retrocopy	retro_sscr_181 ,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,