RetrogeneDB ID: retro_sscr_302

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:33968025..33968487(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000017618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSSSCG00000002004
• Aliases: None
• Description: proteasome activator complex subunit 2 [Source:RefSeq peptide;Acc:NP_999444]

Sequence

>retro_sscr_302
AAGAAAGAAGTCCCTAAGTGTGGCTTTCTCCCTGGGAATGAGAAGGTCCTGGCCTGGCTTGCCCCGGTTCAGCCAGAAGT
CTGGACTCTCAAAGAAAAATGCATTCTGGTGAGCACAGGGACCCAGCACCTGACCCCCAAAATTGAGGATGGAAATGACT
TTGGGGTGGCAGTCCAGGAAAACGTGCTGGAGGGGGTAAATGAAGTCAAGACCAAAGTAGAAGCCCTTCTAGACACCATT
TCCAAGTACTTCTCAGAAAGCAGGGATGCTGCGGCCAAGGCCCCTAAGGAGACCAACGTAGTGGATCACTGGGCCCTGGT
GCCCGAGCGAGACGAGGCAGCCTATGAGGAGCTCAGGGCCATGGTGCTGAACCTGAGGACCTTCTATGCTGAACTTGACC
ATATTATCAGCAGCAACCTGGAGTAAATTGTCAGCCCAACGTGGGGGGAGAAGCCATCAATG

Alignment

ORF - retro_sscr_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 61.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RERVPKCGFLPGNEKILALLGLVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGVAVQEKVLERVNAVK
          ...VPKCGFLPGNEK.LA.L..V.PEVWTLKEKCILV.T..QHL.PKIEDGNDFGVAVQE.VLE.VN.VK
Retrocopy KKEVPKCGFLPGNEKVLAWLAPVQPEVWTLKEKCILVSTGTQHLTPKIEDGNDFGVAVQENVLEGVNEVK

Parental  TKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAHGELRAMVLDLRAFYAELYHIISSNL
          TKVEA...TISKYFSE..DA.AKA.KET.V.D..ALV.ERDEAA..ELRAMVL.LR.FYAEL.HIISSNL
Retrocopy TKVEALLDTISKYFSESRDAAAKAPKETNVVDHWALVPERDEAAYEELRAMVLNLRTFYAELDHIISSNL

Parental  EKIVNPKGEEKPSM
          E.IV.P...EKPSM
Retrocopy E*IVSPTWGEKPSM

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	9.42 RPM
SRP014902_testis	0.14 RPM	29.28 RPM
SRP018288_heart	0.00 RPM	34.26 RPM
SRP018288_kidney	0.00 RPM	39.60 RPM
SRP018288_liver	0.32 RPM	45.25 RPM
SRP018288_lung	0.00 RPM	80.14 RPM
SRP018856_adipose	0.35 RPM	75.15 RPM
SRP035408_brain	0.00 RPM	12.10 RPM
SRP035408_liver	0.09 RPM	53.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_302 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_302 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Felis catus	ENSFCAG00000005585	1 retrocopy	retro_fcat_1605,
Myotis lucifugus	ENSMLUG00000009769	1 retrocopy	retro_mluc_2172,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Sus scrofa	ENSSSCG00000002004	1 retrocopy	retro_sscr_302 ,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,