RetrogeneDB ID: retro_sscr_50

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:56141746..56144179(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012359
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZXDC
• Ensembl ID: ENSSSCG00000001824
• Aliases: None
• Description: ZXD family zinc finger C [Source:HGNC Symbol;Acc:28160]

Sequence

>retro_sscr_50
ATGGAAATCCCGAGGCTGCTCCCGGCTCGCGGGACGCGACAGGGCGGCGGCGCTGGCAGCCCCGGGGGCGGCGGCCGGAT
CCACGGAGGTCCTGACCCGCGGGCGGGCCAGGCCCCCGCGCGCCGCCTCCTGCTGCTCCGGGGCCCCCAAGATGGCGGGT
CCGGGCGGCGGCGTGAGGAGGCCCGCGCGGCCTCCTCGGGCCCCGGCCAGAGCCCGTCGGCGCCTAGGCCCGATCGCGGC
AGCGGCGGCGGCGGCAGTGGCGGCGGCGATGACTTCTTCCTGGTGCTTCTGGACCCGGTGGGTGGAGACGTAGAGACCGC
GGGCGCGGGCCAGGCCGCAGGGCCCGTGTGGAGGGAGGAGGCCGGGCTGGGCCCGCGGCTCCAGGGGGGCGAAAGCGGCG
CGAACCCTGAGGGCCGCCCTGCGCTGGGCCCCAGCTGCCTGTCTGTTATCCCCGCCCCAGTCCCGGCCCTGGCCCCGATC
CCCGCCCCAGGCCTGGGCCCCGCCGCGGCCTTCGCGGGCACCGTCACTATTCACAACCAAAACCTGCTGTTGCGTTTGGA
GAACGGCGTCCTCACCCTGGCCACGCCCCCGCCGCCAGCCTGGGCGCCTGGGGTCGCCCCTACCCCTCAGCCCCGGGGTC
TGATCGCCCCGCAAGCGGGTATCCCGCATGCCGCGCAGCCTGGCGACTGTCCCGAGCTGCCGCCAGACCTCCTGCTGGCC
GAGCGGGCGGAACCCGCGCCGGCCCCAGCGCCCGAGGCGGAGGCGGAGGGCCCAGCTGCTGCTGAGAGCCCCCGCGGGCC
CCCTGGGCCGGGCCAGGGCGTGGTGCTGTACCTGTGTCCCGAGGCGCAGTGCGGACAAACCTTCGCCAAGAAGCACCAGC
TGAAGGTGCACCTGCTGACGCACAGCAGCAGCCAGGGCCAGCGGCCCTTCAAGTGCCCCCTGGGCGGCTGCGGCTGGACT
TTCACCACCTCGTACAAGCTCAAGAGACACCTGCAGTCACACGACAAACTGAGGCCCTTTGGGTGCCCTGCAGAGGGCTG
TGGCAAGAGCTTCACCACCGTGTATAACCTCAAAGCACACATGAAGGGCCACGAACAGGAGAACTCATTCAAATGTGAGG
TGTGTGAGGAGACTTTCCCCACACAGGCCAAACTCAGCGCCCACCAGCGCAGCCACTTTGAGCCAGAGAGGCCCTATCAG
TGCGCGTTTTCGGGCTGCAAGAAGACGTTTATCACAGTGAGTGCCCTCTTTTCCCATAACCGCGCCCACTTCAGGGAACA
GGAACTCTTTTCCTGCTCCTTCCCTGGTTGCAGCAAACAGTACGACAAGGCTTGTAGGCTGAAAATTCACCTTCGGAGCC
ACACTGGCGAGAGACCGTTCCTTTGTGATTTTGAGGGCTGTGGCTGGAACTTCACCAGCATGTCCAAACTCCTAAGGCAC
AAAAGGAAGCACGATGATGATCGGAGGTTCATGTGCCCTGTGGAAGGCTGTGGGAAATCTTTCACAAGGGCCGAGCATCT
CAAAGGCCACAGCATAACCCACCTGGGCACAAAGCCTTTTGTGTGTCCCGTGGAGGGCTGTTGTGCCAGGTTCTCTGCTC
GCAGTAGTCTCTACATTCACTCCAAAAAACACTTGCAGGATGTGGACACTTGGAAAAGCCGATGCCCAGTCTCCACTTGT
AATAAACTCTTCACATCCAAGCATAGCATGAAGACCCACATGGCCAAAAGGCACAACCTGCGCCAGGATCTCCTAGCTCA
GCTAGAAGCTGCAAATTCTCTTACGCCCAGCAGTGAACTTACCAGCCAGGGGCAGAATGACCTCAGTGAGGCAGAGCTTG
TGTCTCTCTTCTCTGATGCACCTGGTAATAGTTCTGCTGCAGTCCTGGACACAGCATTGGTGAACTCTGGGATCTTGACT
ATTGATGTGGCTTCTGTGAACTCAACTCTGGCAGGGAACCATGTCCCTGCTAGTAATAATAATTCCTTAGGGCAGGCAGT
GGATCCTCCCGCCTTGATGGCCACAGGTGACCTTCCTCAAAGTCTGGATACCTCACTCTTTTTTGGAACAACAGCCGCCG
GTTTTCAGCAGAGCCCCTTAGATATGGATGATGTCTCAACTCTAAGTGTGGGGACATTGGGATCTCTGGGCTCTTTGGCT
ATGAAAAACTCGAGTCAAGAGCCCCAGGCGTTGACTCCCAGCAGTAAGCTAACAGCAGACACAGATGCTCTGACTCCTTC
AAGCACCCTTTGTGAAAGCAGTGTCTCAGAACTACTGCCGCCAACCAAAACGGAATGGAATGTACATCCTGACTCTGACT
TTTTTGGACAAGAGGAAGAAACCCAGTTTGGATTCTCCAATCCAGCAGGGAACCATGGGTCTCAGAAAGAAACAGATCTT
ATCACAGTGACTGGCAGCTCATTTTTGGTATAA

Alignment

ORF - retro_sscr_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.54 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YRCPEPQCALLFAKKHQLKVHLLTHSGGQGRRPFKCPLDGCGWAFTTSYKLKRHLQSHDKLRPFGCPVGG
          Y.CPE.QC...FAKKHQLKVHLLTHS..QG.RPFKCPL.GCGW.FTTSYKLKRHLQSHDKLRPFGCP..G
Retrocopy YLCPEAQCGQTFAKKHQLKVHLLTHSSSQGQRPFKCPLGGCGWTFTTSYKLKRHLQSHDKLRPFGCPAEG

Parental  CGKKFTTVYNLKAHMKGHEQESLFKCEVCAERFPTHAKLSSHQRSHFEPERPYKCDYPGCEKTFITVSAL
          CGK.FTTVYNLKAHMKGHEQE..FKCEVC.E.FPT.AKLS.HQRSHFEPERPY.C...GC.KTFITVSAL
Retrocopy CGKSFTTVYNLKAHMKGHEQENSFKCEVCEETFPTQAKLSAHQRSHFEPERPYQCAFSGCKKTFITVSAL

Parental  FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFICDSDSCGWTFTSMSKLLRHKRKHED
          FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPF.CD...CGW.FTSMSKLLRHKRKH.D
Retrocopy FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFLCDFEGCGWNFTSMSKLLRHKRKHDD

Parental  DRRFACPVEGCGKSFTRAEHLKGHSVTHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVAP-KSRCP
          DRRF.CPVEGCGKSFTRAEHLKGHS.THLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDV...KSRCP
Retrocopy DRRFMCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVDTWKSRCP

Parental  ASSCDRLFASKHNGKAHVGRQPRRHPDLFPPLGAPSALTPSSDLSGPGQSEFSNVDLALLFSDTPGDNSG
          .S.C..LF.SKH..K.H.........DL...L.A...LTPSS.L...GQ...S...L..LFSD.PG.NS.
Retrocopy VSTCNKLFTSKHSMKTHMAKRHNLRQDLLAQLEAANSLTPSSELTSQGQNDLSEAELVSLFSDAPG-NSS

Parental  AAGASDEALSAGILTIDVTSMSSSLGGD-LPTS-HTSLG-PMDPLVLVAHSDVPPGPDSPLVLGTAATVL
          AA.........GILTIDV.S..S.L.G...P.S...SLG...DP..L.A..D.P...D..L..GT.A...
Retrocopy AAVLDTALVNSGILTIDVASVNSTLAGNHVPASNNNSLGQAVDPPALMATGDLPQSLDTSLFFGTTAAGF

Parental  QQRSFAMDDTQGVGAGALGCLVAVPVKSLSLDPPALTSGSSSAANTCMPASASSTQGNTSVPELLVPIKV
          QQ....MDD......G.LG.L.....K..S..P.ALT..S...A.T......SST....SV.ELL.P.K.
Retrocopy QQSPLDMDDVSTLSVGTLGSLGSLAMKNSSQEPQALTPSSKLTADT-DALTPSSTLCESSVSELLPPTKT

Parental  EADSPPGPDTIRQQERSR
          E....P..D...Q.E...
Retrocopy EWNVHPDSDFFGQEEETQ

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	5.31 RPM	80.30 RPM
SRP014902_testis	41.02 RPM	132.11 RPM
SRP018288_heart	5.47 RPM	14.41 RPM
SRP018288_kidney	6.50 RPM	36.35 RPM
SRP018288_liver	2.88 RPM	16.31 RPM
SRP018288_lung	16.09 RPM	46.94 RPM
SRP018856_adipose	11.63 RPM	22.13 RPM
SRP035408_brain	3.59 RPM	38.30 RPM
SRP035408_liver	1.41 RPM	19.40 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_sscr_50 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI346972	56142725	56143267	99.9	541	1	540
EW000871	56142712	56143316	99.9	603	1	602

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_50 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006438	1 retrocopy	retro_amel_1830,
Equus caballus	ENSECAG00000026954	2 retrocopies	retro_ecab_1064, retro_ecab_1107,
Mus musculus	ENSMUSG00000034430	1 retrocopy	retro_mmus_44,
Rattus norvegicus	ENSRNOG00000025818	1 retrocopy	retro_rnor_2933,
Sus scrofa	ENSSSCG00000001824	1 retrocopy	retro_sscr_50 ,
Ictidomys tridecemlineatus	ENSSTOG00000007207	1 retrocopy	retro_itri_60,