RetrogeneDB ID: retro_sscr_854

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:151213704..151214154(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME2
• Ensembl ID: ENSSSCG00000017591
• Aliases: None
• Description: Sus scrofa non-metastatic cells 2, protein (NM23B) expressed in (NME2), mRNA. [Source:RefSeq mRNA;Acc:NM_001044610]

Sequence

>retro_sscr_854
GCCTACAGGGACCACACCTTCATTGCCTGCCCCCTGGAGGGCAGGCAGCTTGGCCAGGTGGGACGAGACCATCAAGTGTT
TCCAGCAGAAGGGATTCTGCCTCATGGGCACGGAAGTTCCTTCAGGCCTCCGAGGGCCTCGAAAGCAGCACAACGCTGAC
CTGAATGGCCACCCACTCCCCTCGAGGCTGGAGAAGCGCATGGACTCAGGGCCCTGCTGTGGCCATGGTCTGGAGGGGCT
GAATGTGGTATAGACAGGGAGAGGGATGCCTGGGGAGACCCATCCAGCAGAATCTAAGTCGAGCACGATATGAGGGGATG
TCCTCATTCAAGGCGGCAGGAACATCGTTCATAGCAGTGATTCAGTAAAAAGAGCTGGGGAAGACGTCAGCCTACGGTTT
AAGTCTGGAGAAGTGGGGACTACAAGACTTGTGCCTTTGCCGGAATCTAT

Alignment

ORF - retro_sscr_854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AHAERTFIAVKPDGVQRGLVG-EIIKRFEQKGFRLV-ALKFLQASEEL-LKQHYIDLKDRPFFPGLVKYM
          A....TFIA....G.Q.G.VG.E.IK.F.QKGF.L..A.KFLQASE.L..KQH..DL...P....L.K.M
Retrocopy AYRDHTFIACPLEGRQLGQVG>ETIKCFQQKGFCLM>ARKFLQASEGL<RKQHNADLNGHPLPSRLEKRM

Parental  GSGP-VVAMVW-EGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKP
          .SGP..VAMVW.EGLNVV.TGR.M.GET.PA.SK..TI.GD..IQ.GRNI.H.SDSVK.A....SL.FK.
Retrocopy DSGP>AVAMVW<EGLNVV*TGRGMPGETHPAESKSSTI*GDVLIQGGRNIVHSSDSVKRAGEDVSLRFKS

Parental  EEL-VEYKSCAFDWIY
          .E....YK.CAF..IY
Retrocopy GEV<GDYKTCAFAGIY

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	176.80 RPM
SRP014902_testis	0.00 RPM	127.73 RPM
SRP018288_heart	0.00 RPM	115.28 RPM
SRP018288_kidney	0.20 RPM	203.32 RPM
SRP018288_liver	0.00 RPM	110.34 RPM
SRP018288_lung	0.10 RPM	101.93 RPM
SRP018856_adipose	0.60 RPM	187.10 RPM
SRP035408_brain	0.03 RPM	131.58 RPM
SRP035408_liver	0.00 RPM	143.40 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_854 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_854 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_676

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Otolemur garnettii	ENSOGAG00000025331	9 retrocopies	retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Sus scrofa	ENSSSCG00000011347	1 retrocopy	retro_sscr_1076,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854 ,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,