RetrogeneDB ID: retro_sscr_163

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:86159126..86159471(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000004396
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSSSCG00000017936
• Aliases: None
• Description: Sus scrofa GABA(A) receptor-associated protein (GABARAP), mRNA. [Source:RefSeq mRNA;Acc:NM_001190288]

Sequence

>retro_sscr_163
ATGAAGTTCGTGTATAAAGAGGAGCATCCATTTGAGAAGGGGTGCACTGAGGGCAAGAAGATCCGAAAGAAAGACTCAGA
CTGGGTGCTGGTGATAGTAGAAGAGGCTCCCAAACCTCAGAGAGGAGACCTAGATAAAAAGAAATACCTGGTGCCTTCTG
ATCTCATAATTGGTCAGTTCTACTTCTTGATCTGGAAGCGAATTCATCTCCAAGCTGAGGATGCCTTATTTTTCTTTGTC
AACAATGTCTTACCACCCACCAGTGCCATGATGGGTCAGCTACGCCAGGAACACCATGAAGCAGACTTCTTTCTGTACAT
TACCTACAGTGATGAAAGTGTCTGG

Alignment

ORF - retro_sscr_163 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.87 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKFVYKEEHPFEK...EG.KIRKK..D.V.VIVE.APK...GDLDKKKYLVPSDL..GQFYFLI.KRIHL
Retrocopy MKFVYKEEHPFEKGCTEGKKIRKKDSDWVLVIVEEAPKPQRGDLDKKKYLVPSDLIIGQFYFLIWKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVY
          .AEDALFFFVNNV.PPTSA.MGQL.QEHHE.DFFLYI.YSDESV.
Retrocopy QAEDALFFFVNNVLPPTSAMMGQLRQEHHEADFFLYITYSDESVW

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	0.40 RPM
SRP014902_testis	0.00 RPM	0.57 RPM
SRP018288_heart	0.03 RPM	0.10 RPM
SRP018288_kidney	0.00 RPM	0.99 RPM
SRP018288_liver	0.00 RPM	1.28 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.21 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_163 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014883	1 retrocopy	retro_btau_905,
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Dipodomys ordii	ENSDORG00000005229	1 retrocopy	retro_dord_308,
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562, retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mustela putorius furo	ENSMPUG00000010473	2 retrocopies	retro_mputfur_1290, retro_mputfur_258,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Otolemur garnettii	ENSOGAG00000004388	2 retrocopies	retro_ogar_1212, retro_ogar_1224,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000002655	2 retrocopies	retro_sscr_188, retro_sscr_737,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163 ,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,