RetrogeneDB ID: retro_sscr_36

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:54301871..54302819(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000020805
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSSSCG00000015101
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_sscr_36
ATGGACCTAAAACTAAAAAATCCTGACTTTTGGTACAGTCTCCATGGCCAAGTCCCAGGGCTGCTGGACTGGGACATGGG
AAATGAGTTCTTCCTGCCATGCACCACAGACCAATGCCCCTTAGCTGAGCAGAATCTTGCCAAATACAGACTGCGAGTAA
TGGAGTCCCCAAAGGTACCTCAAGAGAAAAGACCCAGTCCTGGCAAAGATGGTCCTAACTCTGAACCCAACCTGTGGATG
TGGGTGAATCCCAACATTGTGTGCCCCTTTGGCAGCCAGGAAGCCTCAAAGCCCAGTAAAAGAAAGAATGTGGCAAGCAT
ATTTCCTTCCCCTCAGCTCCTCCCAAAGGATGAAGAGTCTAACTGCTCAGAGGCCATAGTGATGGAGTCCCTGCCATCTT
CCTCCGGCAAGCAATCTCCCCCACAAAAGCGGCTCACCTCTTCCCCCAGTGACTGGGAGCTCACAGAAGAGGAGACTGGG
GAACAAGATAACAACTCTTCTGTGGCCCTCAAATCTCCAAACAAAGAATGCTTCCATAGCCAGAAGCTATGGCAAGGCGA
CAGCCAAGAGAGGAAATCTTGGCCCCGCCCCCCCCTCAATTACAGTCACCTAATTGCCCTGGCACTAAGAAACAGCCCTC
CCTGTGGCCTCAATGTGCAAGAGATCTACAGTTTCACACAACAGCATTTCCCTTTTTTCTGGACAGCTCCTGATGGCTGG
AAGAACACCATCCGACACAACCTCTGCTTCCTGGGCAGCTTTGAGAAGGTGCCAGTCAGCCTTCCAGATGGGGCCAATGC
AAAGCCAAGGTCTGGCCTCTGGAGGCTTACTGAGGAGGGACACCGCCGCTTTCAAGAGGAGACTCGTGCCTTAGCCTCCG
CTCGTAGGGAGAGCATCCAACAGTGCATGAGCCAGCCAGATGTGATGACCTCCCTTTTTGGCCTTTGA

Alignment

ORF - retro_sscr_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLKLQHLDFWASLHGQVPGLLDWDMGNESFLAFTTTHLPLAEQNLARYKLRIVEPPKLPLGKKPNPDND
          .DLKL...DFW.SLHGQVPGLLDWDMGNE.FL..TT...PLAEQNLA.Y.LR..E.PK.P..K.P.P..D
Retrocopy MDLKLKNPDFWYSLHGQVPGLLDWDMGNEFFLPCTTDQCPLAEQNLAKYRLRVMESPKVPQEKRPSPGKD

Parental  GPDFEPNLWMWVDPNIVLPPGKLEVPQPSKGENLTSTVPSPQLSPKEEDFARYAEATVVES-PSPSREQS
          GP..EPNLWMWV.PNIV.P.G..E...PSK..N..S..PSPQL.PK.E......EA.V.ES.PS.S..QS
Retrocopy GPNSEPNLWMWVNPNIVCPFGSQEASKPSKRKNVASIFPSPQLLPKDEE-SNCSEAIVMESLPSSSGKQS

Parental  PPRKRFASSPSTWELTEEEEAENQDDSSSVALPSPHKRAPLQSRRLRQTNSQAGRLWSRPPLNYFHLIAL
          PP.KR..SSPS.WELTEEE..E.QD..SSVAL.SP.K.....S..L.Q..SQ....W.RPPLNY.HLIAL
Retrocopy PPQKRLTSSPSDWELTEEETGE-QDNNSSVALKSPNKEC-FHSQKLWQGDSQERKSWPRPPLNYSHLIAL

Parental  ALRNSSPCGLNVQQIYSFTRQHFPFFRTAPEGWKNTVRHNLCFRDCFEKVPVSMQGGAPTRPRSCLWKLT
          ALRNS.PCGLNVQ.IYSFT.QHFPFF.TAP.GWKNT.RHNLCF...FEKVPVS...GA...PRS.LW.LT
Retrocopy ALRNSPPCGLNVQEIYSFTQQHFPFFWTAPDGWKNTIRHNLCFLGSFEKVPVSLPDGANAKPRSGLWRLT

Parental  EEGHRRFVEEVRALASTRLESIQQCMSQPDVMPFLFDL
          EEGHRRF.EE.RALAS.R.ESIQQCMSQPDVM..LF.L
Retrocopy EEGHRRFQEETRALASARRESIQQCMSQPDVMTSLFGL

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	0.00 RPM
SRP014902_testis	0.28 RPM	1.98 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.03 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_36 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_36 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36 ,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,