RetrogeneDB ID: retro_sscr_48

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:41995358..41995655(-)
• Located in intron of: ENSSSCG00000008031

Retrocopy information

• Ensembl ID: ENSSSCG00000027246
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000014371
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Source:UniProtKB/TrEMBL;Acc:F1RGE3]

Sequence

>retro_sscr_48
ATGGCAGCAGCCGCAGCGAGTCGAGGGATCCGCGCCAAATTGGGCCTGCGTGAGATTTGCATCCATGTATGTCAGCACTC
TCCTGGCAGCCAGGGCGTCAGGACTTCATCGAGAAACACTGTGGAGCTGAAGAAGGCGAACCCCGACCTGCCCATCCTCA
TCCGCGAGTGCTCTGATGTGCAGCCCAAGCTCTGGGCTCGCTACGCGTTTGGCCAAGAGAAGAATGTCTCTTTGAACAAC
TTCAGTGCTGATCAGGTAACCAGAACCCTGGAGAATGTGCTAAGCGGCAGAGCCTGA

Alignment

ORF - retro_sscr_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAASRGIRAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYA
          MAAAAASRGIRAKLGLREI.IH.CQ.SPGSQGVR.......VELKKANPDLPILIRECSDVQPKLWARYA
Retrocopy MAAAAASRGIRAKLGLREICIHVCQHSPGSQGVRTS-SRNTVELKKANPDLPILIRECSDVQPKLWARYA

Parental  FGQEKNVSLNNFSADQVTRTLENVLSGKA
          FGQEKNVSLNNFSADQVTRTLENVLSG.A
Retrocopy FGQEKNVSLNNFSADQVTRTLENVLSGRA

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	23.23 RPM
SRP014902_testis	0.14 RPM	34.09 RPM
SRP018288_heart	0.05 RPM	39.68 RPM
SRP018288_kidney	0.10 RPM	35.76 RPM
SRP018288_liver	0.00 RPM	23.03 RPM
SRP018288_lung	0.10 RPM	5.91 RPM
SRP018856_adipose	0.02 RPM	30.96 RPM
SRP035408_brain	0.10 RPM	15.37 RPM
SRP035408_liver	0.03 RPM	7.72 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_48 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_48 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_48 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015041	2 retrocopies	retro_btau_124, retro_btau_151,
Canis familiaris	ENSCAFG00000005861	1 retrocopy	retro_cfam_1343,
Callithrix jacchus	ENSCJAG00000016525	1 retrocopy	retro_cjac_3326,
Cavia porcellus	ENSCPOG00000009178	2 retrocopies	retro_cpor_1045, retro_cpor_1290,
Latimeria chalumnae	ENSLACG00000005796	1 retrocopy	retro_lcha_48,
Mus musculus	ENSMUSG00000014294	1 retrocopy	retro_mmus_2579,
Nomascus leucogenys	ENSNLEG00000009325	1 retrocopy	retro_nleu_67,
Otolemur garnettii	ENSOGAG00000027727	1 retrocopy	retro_ogar_1633,
Pongo abelii	ENSPPYG00000015860	1 retrocopy	retro_pabe_938,
Rattus norvegicus	ENSRNOG00000017571	1 retrocopy	retro_rnor_262,
Sus scrofa	ENSSSCG00000014371	1 retrocopy	retro_sscr_48 ,
Tupaia belangeri	ENSTBEG00000005978	1 retrocopy	retro_tbel_2688,