RetrogeneDB ID: retro_sscr_746

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:623402..623723(+)
• Located in intron of: ENSSSCG00000005917

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000009907
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit C, mitochondrial [Source:UniProtKB/TrEMBL;Acc:F1RJI9]

Sequence

>retro_sscr_746
ATGTGGGCTCGGGCCGTGTGTCTGGGCCTTCTGGCCTTGGCAGCTGGGTGCGGGAGCTTCACCTCCAAGGCGGATCCTCG
GGGAAGGGGTCAGATCACGGCCGGGCTGATGGAGCGCCCGCGGCGGCTAGCGCTTGGGGACTCTGGCAGCCCGGAGGCTG
TAGCATGCTTGCAGAAAGCAATGGCCTTTGCCCGCTGGCCCTGCACCGTGGCCCTGGACGGGGTGGAGCCCACAGAGTCA
GTCTTGGCGGACAGATGTGTGCCCTTGAGCCGTGACAATGGGGCAGAGGGCAGCTGTGCTGAAGAACTGCTAAGAAGCTC
C

Alignment

ORF - retro_sscr_746 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 78.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWARAVWLGLRASAGAFRGFTSKADLQGSGRITAELVEHLERLALVDFGNQEAVARLEKAIAFADRLRDV
          MWARAV.LGL.A.A.....FTSKAD..G.G.ITA.L.E...RLAL.D.G..EAVA.L.KA.AFA.....V
Retrocopy MWARAVCLGLLALAAGCGSFTSKADPRGRGQITAGLMERPRRLALGDSGSPEAVACLQKAMAFARWPCTV

Parental  DTDGVEPMDSVLEDRCLYLRSDNVVEGNCAEELLQNS
          ..DGVEP..SVL.DRC..L..DN..EG.CAEELL..S
Retrocopy ALDGVEPTESVLADRCVPLSRDNGAEGSCAEELLRSS

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	0.13 RPM	8.10 RPM
SRP014902_testis	0.28 RPM	26.03 RPM
SRP018288_heart	0.13 RPM	8.46 RPM
SRP018288_kidney	0.20 RPM	16.06 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.20 RPM	11.91 RPM
SRP018856_adipose	0.00 RPM	16.19 RPM
SRP035408_brain	0.00 RPM	9.15 RPM
SRP035408_liver	0.06 RPM	8.98 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_746 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_746 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585, retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746 ,
Tarsius syrichta	ENSTSYG00000006845	1 retrocopy	retro_tsyr_1219,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,