RetrogeneDB ID: retro_sscr_944

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:84473847..84474237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000017352
• Aliases: None
• Description: None

Sequence

>retro_sscr_944
GTTGTCACCACAGTGAATAAGAAGATGAGGTCCAGGTTGTTGCCACCTTCATGAGAAGCAGGCATAGATCATGATGAAGC
CCAGGATAGTGTCAGAGGAGGAGAAACAGAGGGAAGCTGCACCCCTGGCCATGTATGCTGATGTGTGAGACAAAGACAAT
AAAGCAGATGAGAAGGATGATTCAGGTGAGGCCATGATGAAGGTTCTGGCAAATCTCTGCTCCAAAACACCCATGTGGAA
GATGTCCCAAGTGCTGGAAAACTGGAGCAAGACTCACTCTGGGATGAGTCCCAGAGGAAGAAGGAATAGGATAAGCTGCA
GAAGGAGAGGGACAAACTAACCAAAGAGGAGTGCAAGGAAAAGAATAAGAAAAGGACAGAAAGAAGGGAG

Alignment

ORF - retro_sscr_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 59.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTTKVKK-EDEVQAIATLI-EKQAQIVVKPRMVSEEEKQRKAALLAQYADVTDEEQWEADEKDDSGASTM
          V.T.V.K.EDEVQ..AT...EKQA.I..KPR.VSEEEKQR.AA.LA.YADV.D.....ADEK.D.....M
Retrocopy VVTTVNK<EDEVQVVATFM<EKQA*IMMKPRIVSEEEKQREAAPLAMYADV*DKDN-KADEK-DDSGEAM

Parental  -NLGSDKSLFRNTNVEDVLNARKLERDSLRDESQRKKEQDKLQRERDKLAKQERKEKEKKRTQRGE
          ...GS.KSL..NT.VEDV..A.KLE.DSL.DESQRKKE.DKLQ.ERDKL.K.E.KEK.KKRT.R.E
Retrocopy <DEGSGKSLLQNTHVEDVPSAGKLEQDSLWDESQRKKE*DKLQKERDKLTKEECKEKNKKRTERRE

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	2.79 RPM
SRP014902_testis	0.00 RPM	8.49 RPM
SRP018288_heart	0.00 RPM	10.50 RPM
SRP018288_kidney	0.00 RPM	11.33 RPM
SRP018288_liver	0.00 RPM	4.80 RPM
SRP018288_lung	0.00 RPM	11.10 RPM
SRP018856_adipose	0.03 RPM	11.05 RPM
SRP035408_brain	0.00 RPM	21.50 RPM
SRP035408_liver	0.00 RPM	12.27 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_944 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_944 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173, retro_sscr_944 ,