RetrogeneDB ID: retro_sscr_472

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:121098472..121098971(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL1
• Ensembl ID: ENSSSCG00000030390
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 1 [Source:HGNC Symbol;Acc:9260]

Sequence

>retro_sscr_472
ATGGTGGCTATCCCTCCAGACTCCTGGCAGCTGCCCAACGTATACTTGAAGATCAGCATGGGGATTATTGTGCCAGAGCT
GTATTGGAAGCATGCTCCAAAGACCTGTAAGAACTTGGCTGAATTGGCTCACTGAGGTTACTACAATGGTATCAAATTCC
ACAGAATCACCAAAATCTTTACGGTCTAGGGAGGTGACCCAACAGGAACAGGTTGAGGCGGAGCATCTATCTATGGCAAG
CAGTTTGAAGATGAACTTCATCCCAACTTGAAATTCACAGGGTCTGGAATTCTTGCAATGGCCATTGCAGAGCCAGACAC
CAAACGGCAGCCAGTACTTTGTGACCCTGGCTCCCACGCAGTGGCTTGATGGCAAACACACCATTTTTGGCTGTGTGTGC
CAGGGTATAGGGATGGTGAATCGAGTAGGAATGGTGGAAACAAACTCCCAGGACCGCCCCAAGGACGATGTGAAGATCAT
TAAGGCGTACCCTTCTGGG

Alignment

ORF - retro_sscr_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGT
          M.AIPPDSWQ.PNVYL..SMGIIV.ELYWKHAPKTCKN.AELA..GYYNG.KFHRI.K.F...GGDPTGT
Retrocopy MVAIPPDSWQLPNVYLKISMGIIVPELYWKHAPKTCKNLAELAH*GYYNGIKFHRITKIFTV*GGDPTGT

Parental  GRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDT-NGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMV
          G.GGASIYGKQFEDELHP.LKFTG.GILAMA.A.PDT.NGSQ.FVTLAPTQWLDGKHTIFG.VCQGIGMV
Retrocopy G*GGASIYGKQFEDELHPNLKFTGSGILAMAIAEPDT>NGSQYFVTLAPTQWLDGKHTIFGCVCQGIGMV

Parental  NRVGMVETNSQDRPVDDVKIIKAYPSG
          NRVGMVETNSQDRP.DDVKIIKAYPSG
Retrocopy NRVGMVETNSQDRPKDDVKIIKAYPSG

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	0.13 RPM	9.82 RPM
SRP014902_testis	0.00 RPM	22.91 RPM
SRP018288_heart	0.24 RPM	8.88 RPM
SRP018288_kidney	0.59 RPM	20.19 RPM
SRP018288_liver	0.00 RPM	13.11 RPM
SRP018288_lung	0.10 RPM	18.33 RPM
SRP018856_adipose	0.09 RPM	19.82 RPM
SRP035408_brain	0.00 RPM	19.37 RPM
SRP035408_liver	0.00 RPM	22.72 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_472 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000213	1 retrocopy	retro_amel_30,
Bos taurus	ENSBTAG00000002376	1 retrocopy	retro_btau_854,
Choloepus hoffmanni	ENSCHOG00000006001	1 retrocopy	retro_chof_250,
Callithrix jacchus	ENSCJAG00000016094	1 retrocopy	retro_cjac_1302,
Erinaceus europaeus	ENSEEUG00000009371	1 retrocopy	retro_eeur_204,
Homo sapiens	ENSG00000137168	1 retrocopy	retro_hsap_2086,
Gorilla gorilla	ENSGGOG00000027071	1 retrocopy	retro_ggor_1630,
Loxodonta africana	ENSLAFG00000028161	2 retrocopies	retro_lafr_1187, retro_lafr_435,
Macropus eugenii	ENSMEUG00000000997	1 retrocopy	retro_meug_1008,
Myotis lucifugus	ENSMLUG00000002299	1 retrocopy	retro_mluc_69,
Monodelphis domestica	ENSMODG00000013502	2 retrocopies	retro_mdom_500, retro_mdom_997,
Mustela putorius furo	ENSMPUG00000014166	1 retrocopy	retro_mputfur_29,
Nomascus leucogenys	ENSNLEG00000010779	1 retrocopy	retro_nleu_2135,
Oryctolagus cuniculus	ENSOCUG00000007046	2 retrocopies	retro_ocun_1493, retro_ocun_1759,
Otolemur garnettii	ENSOGAG00000011275	3 retrocopies	retro_ogar_1484, retro_ogar_2850, retro_ogar_939,
Ochotona princeps	ENSOPRG00000006059	3 retrocopies	retro_opri_1054, retro_opri_238, retro_opri_641,
Procavia capensis	ENSPCAG00000015572	1 retrocopy	retro_pcap_426,
Pongo abelii	ENSPPYG00000016554	1 retrocopy	retro_pabe_2009,
Pan troglodytes	ENSPTRG00000018111	1 retrocopy	retro_ptro_1535,
Sus scrofa	ENSSSCG00000030390	1 retrocopy	retro_sscr_472 ,