RetrogeneDB ID: retro_sscr_1085

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL893011.1:79089..79361(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGP
• Ensembl ID: ENSSSCG00000012061
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class P [Source:HGNC Symbol;Acc:3046]

Sequence

>retro_sscr_1085
ATGATAGAAAATTCACCATGGCTGTGATGGAAAGAGCTATTCATCAATGCTTCGTTCTTTTCTTAACTTCCCACTTTAGC
TTCATCCTCTAGCCCATGTAGGCTTTTATTCCTGAAACTTGGCTAAACTTCTTATGTGTAACATATCAGCCTCCAAAATA
TTGGGCAGTTGCACTACCTGTCTACCTCTTTATAATCATTGGCTGCGTGCTCTTTTTTTGGAATTACCTGGTAAGTACCT
TGTCACTCAACTTCATTCGTACAATCACAGAA

Alignment

ORF - retro_sscr_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.51 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVENSP-SPLPERAIYG-FVLFLSSQFGFMLYLVWAFIPESWLNSLGLTYWPQKYWAVALPVYLLITIVI
          M.ENSP.....ERAI...FVLFL.S.F.F.L....AFIPE.WLN.L..TY.P.KYWAVALPVYL...I.I
Retrocopy MIENSP<MAVMERAIHQCFVLFLTSHFSFIL*PM*AFIPETWLNFLCVTYQPPKYWAVALPVYLF--III

Parental  GYVLLFGINMMSTSPLNSIHTITD
          G.VL.F.....ST..LN.I.TIT.
Retrocopy GCVLFFWNYLVSTLSLNFIRTITE

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	14.20 RPM
SRP014902_testis	0.00 RPM	15.56 RPM
SRP018288_heart	0.00 RPM	12.57 RPM
SRP018288_kidney	0.00 RPM	28.17 RPM
SRP018288_liver	0.00 RPM	10.07 RPM
SRP018288_lung	0.00 RPM	7.94 RPM
SRP018856_adipose	0.00 RPM	17.22 RPM
SRP035408_brain	0.00 RPM	11.02 RPM
SRP035408_liver	0.00 RPM	4.46 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1085 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009702	4 retrocopies	retro_cfam_1022, retro_cfam_1559, retro_cfam_1976, retro_cfam_238,
Callithrix jacchus	ENSCJAG00000002683	2 retrocopies	retro_cjac_1276, retro_cjac_2587,
Cavia porcellus	ENSCPOG00000007156	2 retrocopies	retro_cpor_426, retro_cpor_680,
Equus caballus	ENSECAG00000019349	1 retrocopy	retro_ecab_348,
Felis catus	ENSFCAG00000028400	8 retrocopies	retro_fcat_1269, retro_fcat_1286, retro_fcat_1408, retro_fcat_1495, retro_fcat_1671, retro_fcat_181, retro_fcat_1859, retro_fcat_729,
Homo sapiens	ENSG00000185808	4 retrocopies	retro_hsap_163, retro_hsap_1909, retro_hsap_2110, retro_hsap_2423,
Gorilla gorilla	ENSGGOG00000010275	3 retrocopies	retro_ggor_1397, retro_ggor_1508, retro_ggor_1639,
Macaca mulatta	ENSMMUG00000016211	2 retrocopies	retro_mmul_377, retro_mmul_624,
Monodelphis domestica	ENSMODG00000020988	1 retrocopy	retro_mdom_1807,
Mustela putorius furo	ENSMPUG00000008312	5 retrocopies	retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Mus musculus	ENSMUSG00000022940	1 retrocopy	retro_mmus_2841,
Nomascus leucogenys	ENSNLEG00000004523	4 retrocopies	retro_nleu_1235, retro_nleu_1276, retro_nleu_1558, retro_nleu_2444,
Oryctolagus cuniculus	ENSOCUG00000022451	3 retrocopies	retro_ocun_586, retro_ocun_664, retro_ocun_881,
Otolemur garnettii	ENSOGAG00000011097	1 retrocopy	retro_ogar_2382,
Pongo abelii	ENSPPYG00000011409	3 retrocopies	retro_pabe_1787, retro_pabe_1993, retro_pabe_464,
Pan troglodytes	ENSPTRG00000013897	3 retrocopies	retro_ptro_1397, retro_ptro_1547, retro_ptro_156,
Pteropus vampyrus	ENSPVAG00000000857	3 retrocopies	retro_pvam_1100, retro_pvam_1182, retro_pvam_682,
Sarcophilus harrisii	ENSSHAG00000014284	1 retrocopy	retro_shar_548,
Sus scrofa	ENSSSCG00000012061	1 retrocopy	retro_sscr_1085 ,
Ictidomys tridecemlineatus	ENSSTOG00000010943	5 retrocopies	retro_itri_1237, retro_itri_1258, retro_itri_1869, retro_itri_616, retro_itri_897,
Tarsius syrichta	ENSTSYG00000009899	1 retrocopy	retro_tsyr_47,
Tursiops truncatus	ENSTTRG00000007711	3 retrocopies	retro_ttru_1043, retro_ttru_677, retro_ttru_883,