RetrogeneDB ID: retro_hsap_1112

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:48554422..48554887(-)
• Located in intron of: ENSG00000177981

Retrocopy information

• Ensembl ID: ENSG00000258051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSG00000133028
• Aliases: SCO1, SCOD1
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_hsap_1112
GGCCAACTTTGGTGTCTCTTGCCTGGCTGACATGAGCTTTGGGGCCCAGCCAAGTAGACTGTGAGAGTGTTGCCAAGGCA
ATTCTGCATGCAAGAGGAAGTGTGGCAGGACTGGGGGTTTGCTGATAGCTGCCTGGGAAGCTGGCCCCTCAGGCAGTGAT
ACCACCAACCACCCTTGAGGTGGTCAGGGCCTGAGCAGAAGGACTGCAGAGACTGCACATGCCCCTTGAAGCCCAGGCCT
ATTTCTTGGAAGTCTTTAGCATTCACATTTGCTATCTGAGGAGGTTTACTGCCTGGAGTGAAGTATTCAAAATAGAAAAG
ACAGAGAAGCTAGAGAAGGAACAGCAGTGAAGCATCAACAAGCCTTTACTGGGGGACCATTTTCCCTCACAACACATTTG
GAGAGCCTGAAACTGACAAAGACTACCTGGGTCAGTGGCTGTTGATTTATTCTGGTTTCAGTCAT

Alignment

ORF - retro_hsap_1112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.62 %
• Parental protein coverage: 50.5 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GQLWRFLPRGLEFWGPAEGTARVLLRQFCARQAEAWRASGRPGYCLGTRPLST--ARPPPPWS---QKGP
          GQLW..LP...E.WGPA..T.RVL.RQFC..Q.E.W...G....CLG..PL......PP..WS...QK..
Retrocopy GQLWCLLPG*HELWGPAK*TVRVLPRQFCM-QEEVWQDWGFADSCLGSWPLRQ*YHQPPLRWSGPEQKDC

Parental  GDSTRPSKPGPVSWKSLAITFAIGGALLAGMKH-VKKEKAEKLEKERQRHIGKPLL-GGPFSLTTHT-GE
          .D.T.P.KP.P.SWKSLA.TFAI.G.LL.G.K...K.EK.EKLEKE.Q..I.KPLL.GGPFSLTTH..GE
Retrocopy RDCTCPLKPRPISWKSLAFTFAI*GGLLPGVKY<FKIEKTEKLEKEQQ*SINKPLL<GGPFSLTTHL<GE

Parental  RKTDKDYLGQWLLIYFGFTH
          ..TDKDYLGQWLLIY.GF.H
Retrocopy PETDKDYLGQWLLIYSGFSH

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
bodymap2_adipose	0.00 RPM	15.13 RPM
bodymap2_adrenal	0.00 RPM	16.76 RPM
bodymap2_brain	0.00 RPM	13.95 RPM
bodymap2_breast	0.00 RPM	15.45 RPM
bodymap2_colon	0.00 RPM	12.26 RPM
bodymap2_heart	0.00 RPM	19.22 RPM
bodymap2_kidney	0.00 RPM	20.20 RPM
bodymap2_liver	0.00 RPM	13.48 RPM
bodymap2_lung	0.00 RPM	10.36 RPM
bodymap2_lymph_node	0.00 RPM	15.24 RPM
bodymap2_ovary	0.00 RPM	16.94 RPM
bodymap2_prostate	0.00 RPM	14.53 RPM
bodymap2_skeletal_muscle	0.00 RPM	10.99 RPM
bodymap2_testis	0.06 RPM	14.08 RPM
bodymap2_thyroid	0.00 RPM	25.55 RPM
bodymap2_white_blood_cells	0.00 RPM	15.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1112 was not detected

EST

No EST(s) were mapped for retro_hsap_1112 retrocopy.

TSS

No TSS is located nearby retro_hsap_1112 retrocopy 5' end.

Lab

retro_hsap_1112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112 ,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,