RetrogeneDB ID: retro_sscr_160

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:82463919..82464251(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025782
• Aliases: None
• Description: None

Sequence

>retro_sscr_160
GGTCCGGGGGCTGTTTTCCGCAGTTTGGGTGCCTTGTCCGCAGCTGGGGCCTTAGGATTGGCCTCCTACGGAGTGCACAG
AGCCCAGTTTCTGGATGCCTACGGGAAAAGCTCTTTGACAAGGCCAACAAACACCACTTTTTACACAGCCTGGCCCTGTT
AGGGGTGCCCCTGTGCAGAAAACCCCTCTGGGCTGGGTTACTGCTAGCTTCTGGAACCACCTTATTCTGCACCAGCTTTT
ACTACCAGTCTCTTAGCGGAGACCACAGCATCCGGACTTTGGCCCCTGTAAGAGGGAGCCTGCCAATTTGGGGCTGGCTT
GCCTTGGCTCTT

Alignment

ORF - retro_sscr_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPGAVFRRLGALSGAGALGLASYGAHGAQFPDAYGK-ELFDKTNKHHFLHSLALLGVPLCRKPLWAGLLL
          GPGAVFR.LGALS.AGALGLASYG.H.AQF.DAYGK..LFDK.NKHHFLHSLALLGVPLCRKPLWAGLLL
Retrocopy GPGAVFRSLGALSAAGALGLASYGVHRAQFLDAYGK<KLFDKANKHHFLHSLALLGVPLCRKPLWAGLLL

Parental  ASGTTLFCTSFYYQALSGDPSIQTLAPVGGSLLILGWLALAL
          ASGTTLFCTSFYYQ.LSGD.SI.TLAPV.GSL.I.GWLALAL
Retrocopy ASGTTLFCTSFYYQSLSGDHSIRTLAPVRGSLPIWGWLALAL

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	19.38 RPM
SRP014902_testis	0.14 RPM	23.90 RPM
SRP018288_heart	0.00 RPM	8.54 RPM
SRP018288_kidney	0.00 RPM	93.68 RPM
SRP018288_liver	0.00 RPM	17.91 RPM
SRP018288_lung	0.00 RPM	16.90 RPM
SRP018856_adipose	0.00 RPM	59.12 RPM
SRP035408_brain	0.06 RPM	6.45 RPM
SRP035408_liver	0.00 RPM	9.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_160 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016683	5 retrocopies	retro_amel_1190, retro_amel_1360, retro_amel_285, retro_amel_504, retro_amel_577,
Bos taurus	ENSBTAG00000031752	3 retrocopies	retro_btau_1301, retro_btau_1812, retro_btau_532,
Canis familiaris	ENSCAFG00000023205	2 retrocopies	retro_cfam_1146, retro_cfam_1965,
Callithrix jacchus	ENSCJAG00000037786	1 retrocopy	retro_cjac_3985,
Cavia porcellus	ENSCPOG00000004760	1 retrocopy	retro_cpor_564,
Equus caballus	ENSECAG00000016499	1 retrocopy	retro_ecab_682,
Echinops telfairi	ENSETEG00000016076	3 retrocopies	retro_etel_1865, retro_etel_2014, retro_etel_693,
Felis catus	ENSFCAG00000029899	3 retrocopies	retro_fcat_417, retro_fcat_666, retro_fcat_933,
Homo sapiens	ENSG00000205544	2 retrocopies	retro_hsap_2212, retro_hsap_687,
Gorilla gorilla	ENSGGOG00000000113	2 retrocopies	retro_ggor_1745, retro_ggor_590,
Microcebus murinus	ENSMICG00000012550	1 retrocopy	retro_mmur_841,
Macaca mulatta	ENSMMUG00000015618	2 retrocopies	retro_mmul_2408, retro_mmul_929,
Mus musculus	ENSMUSG00000070394	1 retrocopy	retro_mmus_430,
Nomascus leucogenys	ENSNLEG00000009435	2 retrocopies	retro_nleu_2336, retro_nleu_776,
Otolemur garnettii	ENSOGAG00000011378	1 retrocopy	retro_ogar_2039,
Ochotona princeps	ENSOPRG00000014978	2 retrocopies	retro_opri_117, retro_opri_1200,
Pongo abelii	ENSPPYG00000007915	3 retrocopies	retro_pabe_2084, retro_pabe_2179, retro_pabe_536,
Pan troglodytes	ENSPTRG00000030987	2 retrocopies	retro_ptro_1678, retro_ptro_492,
Pteropus vampyrus	ENSPVAG00000005061	1 retrocopy	retro_pvam_357,
Rattus norvegicus	ENSRNOG00000037540	2 retrocopies	retro_rnor_1592, retro_rnor_2896,
Sus scrofa	ENSSSCG00000025782	2 retrocopies	retro_sscr_160 , retro_sscr_330,
Tursiops truncatus	ENSTTRG00000009794	2 retrocopies	retro_ttru_1495, retro_ttru_720,