RetrogeneDB ID: retro_sscr_714

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:107835158..107835753(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000008485
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AK2
• Ensembl ID: ENSSSCG00000024355
• Aliases: None
• Description: adenylate kinase 2 [Source:HGNC Symbol;Acc:362]

Sequence

>retro_sscr_714
CCCAGATTGGCTGAAAACTTCTGTGTCTGTCATTTGGCCACTGGGGACATGCTGAGGGCCATGGTAGCTTCTCGCTCAGA
GCTGGGAAAAAAGCTGAAGTCAACTATGGATGCTGGGAAACTGGTGAGCAATGAAATGTCATGGAGCTCATTGGGAAGAA
TTTGGAGGCCCCTCCATGCAAAAATGGTTTTCTTCCAGGTGGCATCCCTTGGACTGTGAGCAGGCAGAAATGCTTGATGA
CCTCATGGAGAAGAGGAAAGAGAAGCTTGATTCTGTGACTGAATTCAGCATCTCAGACTCTCTGCTGATCCAGAGAATCA
CAGGAAGACTGATTCGCCCCAAGAGTGGCCATTCCTACCACGAGGAGTTCAACTCCACGAAGGAGCCCATGAAAGAGGAC
ATCACTGGGGAACCCTTGAATCGCCAGTCAGATGATAATGAGAAGGCCTTGAAAATCCACCTGGAGGCCTATCACACTCA
GACAACCCCACTGGCGGAGTACTACAGTAAACAGGGCATCCACTCTGCCATCAACACATCCCAGACCCCTGATGTCTTGT
TTGCAAGCATCCTAGCAGCCTTCTCCAAAGCCACA

Alignment

ORF - retro_sscr_714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 80.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PRLAENFCVCHLATGDMLRAMVASGSELGKKLKATMDAGKLVSDEM-VVELIEKNLETPPCKNGFLLDGF
          PRLAENFCVCHLATGDMLRAMVAS.SELGKKLK.TMDAGKLVS.EM.V.ELI.KNLE.PPCKNGFL..G.
Retrocopy PRLAENFCVCHLATGDMLRAMVASRSELGKKLKSTMDAGKLVSNEM<VMELIGKNLEAPPCKNGFLPGGI

Parental  PRTV-RQAEMLDDLMEKRKEKLDSVIEFSIPDALLIRRITGRLIHPKSGRSYHEEFNPPKEPMKDDITGE
          P.TV..QAEMLDDLMEKRKEKLDSV.EFSI.D.LLI.RITGRLI.PKSG.SYHEEFN..KEPMK.DITGE
Retrocopy PWTV<EQAEMLDDLMEKRKEKLDSVTEFSISDSLLIQRITGRLIRPKSGHSYHEEFNSTKEPMKEDITGE

Parental  PLIRRSDDNEKALKIRLEAYHTQTTPLVEYYSKRGIHSAIDASQTPDVVFASILAAFSKAT
          PL.R.SDDNEKALKI.LEAYHTQTTPL.EYYSK.GIHSAI..SQTPDV.FASILAAFSKAT
Retrocopy PLNRQSDDNEKALKIHLEAYHTQTTPLAEYYSKQGIHSAINTSQTPDVLFASILAAFSKAT

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	15.79 RPM
SRP014902_testis	0.00 RPM	23.62 RPM
SRP018288_heart	0.00 RPM	44.14 RPM
SRP018288_kidney	0.00 RPM	84.32 RPM
SRP018288_liver	0.16 RPM	58.21 RPM
SRP018288_lung	0.00 RPM	22.10 RPM
SRP018856_adipose	0.03 RPM	44.16 RPM
SRP035408_brain	0.00 RPM	4.45 RPM
SRP035408_liver	0.21 RPM	107.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_714 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_714 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017605	2 retrocopies	retro_btau_1146, retro_btau_1168,
Canis familiaris	ENSCAFG00000010390	1 retrocopy	retro_cfam_1622,
Callithrix jacchus	ENSCJAG00000001105	1 retrocopy	retro_cjac_509,
Dasypus novemcinctus	ENSDNOG00000014113	4 retrocopies	retro_dnov_1077, retro_dnov_2052, retro_dnov_2690, retro_dnov_588,
Echinops telfairi	ENSETEG00000002333	2 retrocopies	retro_etel_1466, retro_etel_309,
Homo sapiens	ENSG00000004455	1 retrocopy	retro_hsap_395,
Gorilla gorilla	ENSGGOG00000000069	1 retrocopy	retro_ggor_395,
Myotis lucifugus	ENSMLUG00000000793	1 retrocopy	retro_mluc_1463,
Macaca mulatta	ENSMMUG00000006284	1 retrocopy	retro_mmul_1326,
Monodelphis domestica	ENSMODG00000017363	1 retrocopy	retro_mdom_1792,
Nomascus leucogenys	ENSNLEG00000003152	1 retrocopy	retro_nleu_1313,
Oryctolagus cuniculus	ENSOCUG00000001832	2 retrocopies	retro_ocun_1280, retro_ocun_445,
Otolemur garnettii	ENSOGAG00000000818	1 retrocopy	retro_ogar_2760,
Ochotona princeps	ENSOPRG00000005023	1 retrocopy	retro_opri_822,
Pongo abelii	ENSPPYG00000001579	1 retrocopy	retro_pabe_1965,
Pan troglodytes	ENSPTRG00000000499	1 retrocopy	retro_ptro_1587,
Rattus norvegicus	ENSRNOG00000000122	3 retrocopies	retro_rnor_1965, retro_rnor_2315, retro_rnor_974,
Sorex araneus	ENSSARG00000000202	1 retrocopy	retro_sara_556,
Sus scrofa	ENSSSCG00000024355	1 retrocopy	retro_sscr_714 ,
Ictidomys tridecemlineatus	ENSSTOG00000016042	1 retrocopy	retro_itri_595,
Tursiops truncatus	ENSTTRG00000008979	2 retrocopies	retro_ttru_1579, retro_ttru_978,