RetrogeneDB ID: retro_sscr_114

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:78046155..78046622(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNO1
• Ensembl ID: ENSSSCG00000008352
• Aliases: None
• Description: partner of NOB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:32790]

Sequence

>retro_sscr_114
AAGAGGCCCATCTTCCCTCCCTTCTTTGGGGAGGGGTTCCTGGGTGGTCAAGAAGAAAGCAGGAAAATTCCAGTCCCAGG
TAACAAGTCCACACAGTTAAAAGAGAATTGGATGAAGATATTTTTTCCTATTGTGGAGCATTTGGGACTTCAGATACACT
TTAACGTGAAATTGAGGAACGTAGAAATCAGGAGTGGTAAAGAAACCAAGGATGTTAGTGTGCTGACAAAAGCAGTTGAT
TTTGTGAAAGCCTTTATTCTTGGATTTCAGGTGGCGGATGCACTTGCCCTCATTAGGTTGGATGACCTCTTCCTAGAAAC
TTTTGAAATTACAGATGTTAAGCCCTTGAAAGGAAACCACCTGTCCAGGGCAATAGGCAGAATTGCTGGCAAAGGAGGAA
AAACCAAACTCATCATCTAGAATGTAACCCAGATATGAATAGTTTTGCTGATATGAAAGTTCACATC

Alignment

ORF - retro_sscr_114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.53 %
• Parental protein coverage: 61.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRPIFPPLSGDGFLSGKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETK
          KRPIFPP..G.GFL.G.EE.RKIPVP.N..T.LKENWMKIF.PIVEHLGLQI.FN.K.RNVEIR..KETK
Retrocopy KRPIFPPFFGEGFLGGQEESRKIPVPGNKSTQLKENWMKIFFPIVEHLGLQIHFNVKLRNVEIRSGKETK

Parental  DVSALTKAADFVKAFILGFQVEDALALVRLDDLFLETFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIE
          DVS.LTKA.DFVKAFILGFQV.DALAL.RLDDLFLETFEITDVKPLKG.HLSRAIGRIAGKGGKTK..I.
Retrocopy DVSVLTKAVDFVKAFILGFQVADALALIRLDDLFLETFEITDVKPLKGNHLSRAIGRIAGKGGKTKLII*

Parental  NVTRTRIVL-ADVKVHI
          NVT...IVL.AD.KVHI
Retrocopy NVTQI*IVL<ADMKVHI

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	9.42 RPM
SRP014902_testis	0.00 RPM	19.66 RPM
SRP018288_heart	0.00 RPM	9.51 RPM
SRP018288_kidney	0.00 RPM	14.48 RPM
SRP018288_liver	0.00 RPM	9.59 RPM
SRP018288_lung	0.00 RPM	13.34 RPM
SRP018856_adipose	0.00 RPM	8.43 RPM
SRP035408_brain	0.00 RPM	24.49 RPM
SRP035408_liver	0.00 RPM	17.20 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_114 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114 , retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,