RetrogeneDB ID: retro_sscr_1082

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL892872.1:17876..18291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA2
• Ensembl ID: ENSSSCG00000020769
• Aliases: None
• Description: Proteasome subunit alpha type [Source:UniProtKB/TrEMBL;Acc:I3LAB6]

Sequence

>retro_sscr_1082
AAGAAACAGAAATCCATTCTGTAGGATGAGTGAGGTGTACACAAAGTGGAACTGATAACAAAGCATAGAGATTTGGTGTG
GGGGGCATGAGACCAGATTGCTGAGTGCTGGTGCACAGAGCTGGAAAACTAGCTCAACAATGCTACCTTGTTAACCAAGA
ACCCGTTGTCACAGCTCTGCTGGAACAGAGTGTAACTTCTGTGATGCAAGAATATACCCAGTCAGGTGGTGTTCCTCCAC
TCGGAGTTTTTTTTAAACTTATTTGTGGTTGGACTGACAGACAGCCGTGTTTATTTCAGTCAGATCCATCTGGACCTGAC
TTTGCCTGGAAAGTCTATCAGTGGGCAAGAATTATGTGAATAGGGAAATTTTCCTTGAGAAAAGATAGAGCAAAAATCTG
GAACTTAAAGATGCA

Alignment

ORF - retro_sscr_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKQKSILYDERSVHKVEPITKHIGLVYS-GMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVM
          KKQKSIL.DE..VHKVE.ITKH..LV...GM.PD..VLVHRA.KLAQQ.YLV.QEP..TA.L.Q.V.SVM
Retrocopy KKQKSIL*DE*GVHKVELITKHRDLVWG<GMRPDC*VLVHRAGKLAQQCYLVNQEPVVTALLEQSVTSVM

Parental  QEYTQSGGVRPFGVSL-LICGWNEGRPYLFQSDPSGAYFAWK-ATAMGKNYVNGKTFLEKRYNEDLELED
          QEYTQSGGV.P.G....LICGW....P.LFQSDPSG..FAWK.....GKNYVN...FLEKR....LEL.D
Retrocopy QEYTQSGGVPPLGXXXKLICGWTDRQPCLFQSDPSGPDFAWK<SLSVGKNYVNREIFLEKR*SKNLELKD

Parental  A
          A
Retrocopy A

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	44.07 RPM
SRP014902_testis	0.00 RPM	39.89 RPM
SRP018288_heart	0.00 RPM	67.53 RPM
SRP018288_kidney	0.00 RPM	93.97 RPM
SRP018288_liver	0.00 RPM	60.13 RPM
SRP018288_lung	0.00 RPM	29.12 RPM
SRP018856_adipose	0.00 RPM	90.16 RPM
SRP035408_brain	0.00 RPM	65.11 RPM
SRP035408_liver	0.00 RPM	70.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1082 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1082 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_889

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009433	3 retrocopies	retro_amel_1029, retro_amel_1336, retro_amel_1379,
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Mustela putorius furo	ENSMPUG00000018145	1 retrocopy	retro_mputfur_548,
Mus musculus	ENSMUSG00000015671	4 retrocopies	retro_mmus_1104, retro_mmus_1105, retro_mmus_1215, retro_mmus_1320,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Otolemur garnettii	ENSOGAG00000016805	1 retrocopy	retro_ogar_197,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Rattus norvegicus	ENSRNOG00000049920	2 retrocopies	retro_rnor_2041, retro_rnor_2769,
Sus scrofa	ENSSSCG00000020769	3 retrocopies	retro_sscr_1082 , retro_sscr_419, retro_sscr_440,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,