RetrogeneDB ID: retro_sscr_657

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:10060859..10061217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG4
• Ensembl ID: ENSSSCG00000001005
• Aliases: None
• Description: proteasome (prosome, macropain) assembly chaperone 4 [Source:HGNC Symbol;Acc:21108]

Sequence

>retro_sscr_657
ATGGAGGAGCCGCGGGTGGGGGCCGTCTCCCAGAACAACTTCAGAACGAGTCTGTGGGAGCAGATGGTCCACTTCCATGT
CACGCGGCTCATGGACTTGCTCTTCCTGTGGGTCAAGGCCACACGGAAGCTGAGCAACCTTGCCGTGGCCATGTGCACCT
GCTATGAACCCGTCACTATGTCCACGTCCCTCCTCGGGACACATCGGACACGATGTCCACCGGCCTCACCCAGCACTTCG
CCAGGAAGGCCAACAAACAGGTATTTGTCAGCTTTAACCTTCATGGCAGGACGGCGGCTTTGCAGCACTTGTGGAAAACA
GGATTGAGGAGGAAATGGAGGCTTTTTCGGAGCTGTTC

Alignment

ORF - retro_sscr_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGPRAAAAGDVSLHNFTARLWEQLVHFHVMRLTDSLFLWVGATPHLRNLAVAMCTRYDPIPVSTALLG-
          ME.PR..A...VS..NF...LWEQ.VHFHV.RL.D.LFLWV.AT..L.NLAVAMCT.Y.P...ST.LLG.
Retrocopy MEEPRVGA---VSQNNFRTSLWEQMVHFHVTRLMDLLFLWVKATRKLSNLAVAMCTCYEPVTMSTSLLG<

Parental  DTSDPTSTGLAQRLARKTSKQVFVSYNLQN-TDSSFALLVENRIKEEMEAFPEKF
          DTSD..STGL.Q..ARK..KQVFVS.NL....D..FA.LVENRI.EEMEAF.E.F
Retrocopy DTSDTMSTGLTQHFARKANKQVFVSFNLHG<QDGGFAALVENRIEEEMEAFSELF

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	55.75 RPM
SRP014902_testis	0.00 RPM	43.42 RPM
SRP018288_heart	0.00 RPM	7.10 RPM
SRP018288_kidney	0.00 RPM	11.13 RPM
SRP018288_liver	0.00 RPM	8.16 RPM
SRP018288_lung	0.00 RPM	8.04 RPM
SRP018856_adipose	0.00 RPM	11.20 RPM
SRP035408_brain	0.00 RPM	26.49 RPM
SRP035408_liver	0.00 RPM	11.77 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_657 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_657 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014430	1 retrocopy	retro_amel_1196,
Bos taurus	ENSBTAG00000031249	1 retrocopy	retro_btau_1040,
Myotis lucifugus	ENSMLUG00000024906	1 retrocopy	retro_mluc_802,
Rattus norvegicus	ENSRNOG00000039265	2 retrocopies	retro_rnor_1442, retro_rnor_766,
Sus scrofa	ENSSSCG00000001005	3 retrocopies	retro_sscr_362, retro_sscr_656, retro_sscr_657 ,
Tursiops truncatus	ENSTTRG00000006146	2 retrocopies	retro_ttru_1531, retro_ttru_1849,