RetrogeneDB ID: retro_sscr_1093

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL893661.1:35762..36298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf166
• Ensembl ID: ENSSSCG00000005029
• Aliases: None
• Description: chromosome 14 open reading frame 166 [Source:HGNC Symbol;Acc:23169]

Sequence

>retro_sscr_1093
TACCACTGCAACCCTGCCAGCTACACTGTAAAGATGAAATAGAATTTAGAAACTATTGTTGGGCTTGAAGACCAGAAAAT
CAGACATGATGAGATTGAAGACAAATAATTTAAGAAACATCCACAGCAGTAACTAGCCCAAGTTCTTTGAAAAGTATGTC
AGAGACATGAACTGTTCTTTTAAGATTCCAGATCACCAAGTAGCAATTGATGAGCTTCTCGGTTTAACTGTTAGACTTGA
ATGTGGAACATACAAGGACTTGTGACCAGATGTAGGTCATATGCAGACAGTGCAACTAAAAAATGCAGCGTCATTGATCA
TGGATGTGCATAATCCTGGTTGGAAAGCTGATGTAAAGGCTTTGCTAATCTTCTTTAGGTTGGCATCACGATAATTACCT
GGTAACCGTTGAGGCAATTCATATGGTGGTCCAGGAGTTCCTGACACAGGATGCAGCTGCTGGAGCAGATGAAACAAAAG
AAGGTTTGCCTGTTGCTTTAGATGATCATATTCTTGGTTTTGACACAGGAAATGCA

Alignment

ORF - retro_sscr_1093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.42 %
• Parental protein coverage: 75.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YH-NPAGF-NCKDETEFRNF-IVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCPFKIQDRQ
          YH.NPA....CKDE.EFRN.....L...K..........NLRNIHSS..PKFFEKY.RD.NC.FKI.D.Q
Retrocopy YHCNPASY<HCKDEIEFRNY<LLGLKTRKSDMMRLKTN-NLRNIHSSN*PKFFEKYVRDMNCSFKIPDHQ

Parental  EAIDWLLGLAVRLEYGDNAEKYKDLVPDNTKNADNAAKNAEPLINLDVNNPDFKAGVMAL-ANLLQI-QR
          .AID.LLGL.VRLE.G.....YKDL.PD.........KNA..LI..DV.NP..KA.V.AL.ANLL.....
Retrocopy VAIDELLGLTVRLECG----TYKDL*PDVGHMQTVQLKNAASLI-MDVHNPGWKADVKAL<ANLL*V<WH

Parental  HDDYLVMLKAIRILVQERLTQDAVAKANQTKEGLPVALDKHILGFDTGDA
          HD.YLV...AI...VQE.LTQDA.A.A..TKEGLPVALD.HILGFDTG.A
Retrocopy HDNYLVTVEAIHMVVQEFLTQDAAAGADETKEGLPVALDDHILGFDTGNA

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	33.18 RPM
SRP014902_testis	0.00 RPM	53.33 RPM
SRP018288_heart	0.00 RPM	150.25 RPM
SRP018288_kidney	0.00 RPM	144.02 RPM
SRP018288_liver	0.00 RPM	67.96 RPM
SRP018288_lung	0.00 RPM	37.57 RPM
SRP018856_adipose	0.00 RPM	127.52 RPM
SRP035408_brain	0.00 RPM	62.63 RPM
SRP035408_liver	0.00 RPM	64.73 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1093 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1093 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002083	2 retrocopies	retro_amel_224, retro_amel_302,
Canis familiaris	ENSCAFG00000014648	4 retrocopies	retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus	ENSCJAG00000006926	3 retrocopies	retro_cjac_1262, retro_cjac_1947, retro_cjac_3207,
Cavia porcellus	ENSCPOG00000001317	6 retrocopies	retro_cpor_1041, retro_cpor_1177, retro_cpor_1239, retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus	ENSDNOG00000003248	3 retrocopies	retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii	ENSDORG00000012335	1 retrocopy	retro_dord_619,
Erinaceus europaeus	ENSEEUG00000015583	1 retrocopy	retro_eeur_366,
Felis catus	ENSFCAG00000002663	3 retrocopies	retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens	ENSG00000087302	1 retrocopy	retro_hsap_2307,
Loxodonta africana	ENSLAFG00000003162	1 retrocopy	retro_lafr_301,
Microcebus murinus	ENSMICG00000008720	1 retrocopy	retro_mmur_857,
Myotis lucifugus	ENSMLUG00000008643	6 retrocopies	retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta	ENSMMUG00000018200	2 retrocopies	retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica	ENSMODG00000013211	1 retrocopy	retro_mdom_1296,
Mustela putorius furo	ENSMPUG00000005253	6 retrocopies	retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus	ENSMUSG00000021807	2 retrocopies	retro_mmus_140, retro_mmus_3203,
Nomascus leucogenys	ENSNLEG00000012406	1 retrocopy	retro_nleu_2749,
Oryctolagus cuniculus	ENSOCUG00000014681	1 retrocopy	retro_ocun_221,
Otolemur garnettii	ENSOGAG00000013232	5 retrocopies	retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps	ENSOPRG00000016352	2 retrocopies	retro_opri_257, retro_opri_884,
Pongo abelii	ENSPPYG00000005814	1 retrocopy	retro_pabe_1980,
Pan troglodytes	ENSPTRG00000006344	1 retrocopy	retro_ptro_1631,
Sus scrofa	ENSSSCG00000005029	1 retrocopy	retro_sscr_1093 ,
Tupaia belangeri	ENSTBEG00000013898	5 retrocopies	retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta	ENSTSYG00000004528	6 retrocopies	retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus	ENSTTRG00000005721	1 retrocopy	retro_ttru_83,
Vicugna pacos	ENSVPAG00000011443	1 retrocopy	retro_vpac_142,