RetrogeneDB ID: retro_sscr_90

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:81356404..81357280(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000002038
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB8
• Ensembl ID: ENSSSCG00000026951
• Aliases: None
• Description: Sus scrofa proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) (PSMB8), mRNA. [Source:RefSeq mRNA;Acc:NM_213935]

Sequence

>retro_sscr_90
ATGGCTCTGCAGGATGTGTGCCAGTGGCAAGCCTTGGACCCCCAGGGAGCCTCCCCTTACCTGCCTCAGGCTGGTGCTTG
GGCTGTGCCCCGGGGCTGGGACCCTCAGACCTTCCTACAGACCCACGGCCCCAGGCTGGCCCATGGCACCACCACCCTGG
CCTTCCGCTTCCGTGATGGAGTCATTGCTGCGGCTGACACTCGCTCCTCCTGCGGCAACTACGTGGAGTGTCCAGCCTCG
CGCAAGGTCATCCCTGTGCACCAGCACCTCCTGGGCACCACCTCTGGCACCTCAGCCGACTGCACCACCTGGTACCGGGT
GCTGCGGAGGGAGCTGCGGCTACGCGAGCTGAGGGAGGGTCAGCTGCCCAGTGTGGCCGGCGCCGCCAAACTCTTATCTG
GCATGATGTCGCGCTACCGGGGACTGGATCTATGCGTGGCCACCGCCCTGTGCGGCTGGGACCGCTCCGGGCCTGCCCTC
TTCTACGTCTACAGCGACGGCACCCTTCTGCAGGGGGACATCTTCTCGGTGGGCTCTGGATCTCCCTACGCCTATGGTGT
GCTGGATCGCGGCTACCGCTACGACATGAGCACCCAGGAAGCCTACGCCCTGGCCTGCCGCGCTGTGGCTCACGCCACCC
ACCGCGACGCCTACTCGGGGGGCTCCGTAGACCTCTTCCACGTGCGGGAGAGTGGTTGGGAGCACGTGTCCCGCAATGAT
GCCTGGGTGCTGTACTCTGAGCTGCAGAAGCTCTCTGGGCTAGAGAAGGAAGGGGAGGAGGAGGCCACCTCCGAGAGAGC
CGGCCCAGGCAGAGAACCATCTGTGGGACCGGCCCCGGGAGACTTGAGGATGCCTTCAGAAATGGAGAAGCTGTGA

Alignment

ORF - retro_sscr_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.69 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHGTTTLAFKFQHGVIVAVDSRASAGSYIATLRVNKVIEINPYLLGTMSGSAADCQYWERLLAKECRLY
          .AHGTTTLAF.F..GVI.A.D.R.S.G.Y.......KVI.....LLGT.SG..ADC..W.R.L..E.RL.
Retrocopy LAHGTTTLAFRFRDGVIAAADTRSSCGNYVECPASRKVIPVHQHLLGTTSGTSADCTTWYRVLRRELRLR

Parental  YLRNGDRISVSAASKLLSNMMYQYRGMGLSMGSMICGWDKKGPGLYYVDENGTRLSGNMFSTGSGNTYAY
          .LR.G...SV..A.KLLS.MM..YRG..L......CGWD..GP.L.YV...GT.L.G..FS.GSG..YAY
Retrocopy ELREGQLPSVAGAAKLLSGMMSRYRGLDLCVATALCGWDRSGPALFYVYSDGTLLQGDIFSVGSGSPYAY

Parental  GVMDSGHRYDLSIEEAYDLGRRAIVHATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLMHQYREAS
          GV.D.G.RYD.S..EAY.L..RA..HATHRD.YSGG.V...H..E.GW..V...D...L.......S
Retrocopy GVLDRGYRYDMSTQEAYALACRAVAHATHRDAYSGGSVDLFHVRESGWEHVSRNDAWVLYSELQKLS

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_90 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_90 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_90 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_95
Pan troglodytes	retro_ptro_97
Gorilla gorilla	retro_ggor_156
Pongo abelii	retro_pabe_171
Callithrix jacchus	retro_cjac_35
Oryctolagus cuniculus	retro_ocun_176
Bos taurus	retro_btau_11
Canis familiaris	retro_cfam_75
Equus caballus	retro_ecab_18

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102, retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90 ,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,