RetrogeneDB ID: retro_ecab_1064

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:43779034..43780567(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000018848
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZXDC
• Ensembl ID: ENSECAG00000026954
• Aliases: None
• Description: ZXD family zinc finger C [Source:HGNC Symbol;Acc:28160]

Sequence

>retro_ecab_1064
GGCCCGGGCGTAGTGCTGTACCTGTGTCCCGAGGCGCAGTGCGGACAAACCTTCGCCAAGAAGCACCAGCTGAAGGTGCA
CCTGCTGACGCACAGCAGCAACCAGGGCCAACGGCCCTTCAAGTGCCCCCTGGGCGGCTGCGGCTGGACCTTCACCACCT
CGTACAAGCTCAAGAGGCATCTGCAATCACACGACAAACTGCGGCCCTTCGGGTGTCCGGCGGAGGGCTGTGGCAAGAGC
TTCACCACCGTGTATAACCTCAAGGCACACATGAAGGGCCATGAGCAGGAGAACTCTTTCAAATGCGAAGTGTGCGAGGA
GAGCTTCCCCACGCAGGCCAAGCTCAGCGCCCACCAGCGGAGCCACTTTGAGCCGGAGAGGCCCTACCAGTGCGCGTTTT
CTGGCTGCAAGAAGACATTTATCACCGTGAGTGCTCTGTTTTCCCATAACCGCGCCCACTTCAGGGAGCAGGAACTCTTT
TCCTGCTCCTTTCCTGGCTGCAGCAAACAGTACGACAAGGCTTGTCGGCTGAAAATTCACCTGCGGAGCCACACTGGTGA
GAGACCTTTCCTTTGTGACTTTGACGGCTGTGGCTGGAACTTCACTAGCATGTCCAAACTGTTAAGGCACAAAAGGAAGC
ACGACGATGACCGGAGGTTCACGTGCCCTGTGGAAGGCTGTGGGAAATCTTTCACAAGGGCTGAGCATCTGAAAGGCCAC
AGCATAACCCACCTGGGAACAAAGCCCTTTGTGTGCCCCGTGGAAGGCTGCTGTGCCAGGTTCTCTGCTCGAAGTAGCCT
CTACATTCACTCCAAGAAACACTTGCAAGATGTGGACACTTGGAAAAGCCGTTGCCCAGTCTCCACTTGCAATAAACTCT
TCACCTCCAAGCACAGCATGAAGACCCACATGGCCAAAAGGCACAACCTCGGCCAGGATCTCTTAGCTCAGTTAGAAGCG
GCAAATTCTCTTACGCCCAGCAGTGAACTTGCCAGCCAGGGACAGAGTGATCTCAGTGATGCAGAGCTAGTGTCTCTCTT
CTCTGACGTGCCTGGCAGTAGTTCTGCTGCAGTGCTAGACACGGCATTGGTAAACTCTGGAATCTTGACTATTGATGTGG
CTTCGGTGAGCTCAACTCTGGCAGGGAACCTTCCTGCTGCTAATAATAGTTCCTTAGGGCAGGCTCTGGACCCTCGGGGC
TTGATGGCCACCGGTGACCTTCCTCAAAGTCTGGATACCTCTCTCTTTTTTGGAACGACAGCCGCCGGTTTTCAGCAGAG
CCCCTTAGGTATGGATGATGTCTCAAGTCTAAGCGCGGGGCCATTGGGATCTCTGGGATCTTTGGCTATGAAAAACTCAA
GTCAAGAGCCCCAAGCTTTGACCCCCAGCAGTAAGCTAACAGTAGACTCAGATGCTCTGACTCCTTCAAGCACCCTTTGT
GAAAACAGTGTCTCAGATCTACTGACACCAACCAAAGCAGAATGGAACATACATCCTGACTCTGACTTCTTTGGACAGGA
GGAAGAAACCCAG

Alignment

ORF - retro_ecab_1064 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.81 %
• Parental protein coverage: 73.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPAAPRFMSPATQSALSFASKHQLKVHLVTHGGSQG-RPFKCPLDGCGWAFTSSYKLKRHLQSHDKLRPF
          GP.......P..Q....FA.KHQLKVHL.TH...QG.RPFKCPL.GCGW.FT.SYKLKRHLQSHDKLRPF
Retrocopy GPGVVLYLCPEAQCGQTFAKKHQLKVHLLTHSSNQGQRPFKCPLGGCGWTFTTSYKLKRHLQSHDKLRPF

Parental  GCPVGGCGKKFTTVYNLKAHMKGHEQESLFKCEVCAERFPTHAKLSSHQRSHFEPERPYKCDFPGCEKTF
          GCP..GCGK.FTTVYNLKAHMKGHEQE..FKCEVC.E.FPT.AKLS.HQRSHFEPERPY.C.F.GC.KTF
Retrocopy GCPAEGCGKSFTTVYNLKAHMKGHEQENSFKCEVCEESFPTQAKLSAHQRSHFEPERPYQCAFSGCKKTF

Parental  ITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFICDSDSCGWTFTSMSKLLRH
          ITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPF.CD.D.CGW.FTSMSKLLRH
Retrocopy ITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFLCDFDGCGWNFTSMSKLLRH

Parental  KRKHDDDRRFTCSVEGCGKSFTRAEHLKGHSITHLGTKPFECPVEGCCARFSARSSLYIHSKKHLQDVGA
          KRKHDDDRRFTC.VEGCGKSFTRAEHLKGHSITHLGTKPF.CPVEGCCARFSARSSLYIHSKKHLQDV..
Retrocopy KRKHDDDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVDT

Parental  PKSRCPVSSCNRLFTSKHSMKAHVVRQHSRRPDLFPQLGAPSSLTPSSELGGPGQSELNNIDLAALFSDT
          .KSRCPVS.CN.LFTSKHSMK.H....H....DL..QL.A..SLTPSSEL...GQS.L....L..LFSD.
Retrocopy WKSRCPVSTCNKLFTSKHSMKTHMAKRHNLGQDLLAQLEAANSLTPSSELASQGQSDLSDAELVSLFSDV

Parental  PGDGGSAVGASDEALNSGILTIDVTSVSSSLGGNLP-ANNSSLG-PMDPLVLVAHSDIPPGLDSPLVLGT
          PG....AV.......NSGILTIDV.SVSS.L.GNLP.ANNSSLG...DP..L.A..D.P..LD..L..GT
Retrocopy PGSSSAAV-LDTALVNSGILTIDVASVSSTLAGNLPAANNSSLGQALDPRGLMATGDLPQSLDTSLFFGT

Parental  AATVLEQSSFSVDDVQTVSAGALGCLVALPVKDVGQDPEAVTSSSNLAANTTTLTSSSVPQGSTGVPELQ
          .A....QS....DDV...SAG.LG.L..L..K...Q.P.A.T.SS.L......LT.SS.......V..L.
Retrocopy TAAGFQQSPLGMDDVSSLSAGPLGSLGSLAMKNSSQEPQALTPSSKLTVDSDALTPSST-LCENSVSDLL

Parental  APIKVEPASPPGPGAFRQRERSR
          .P.K.E....P....F.Q.E...
Retrocopy TPTKAEWNIHPDSDFFGQEEETQ

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
SRP021940_articular_cartilage	1.59 RPM	33.23 RPM
SRP021940_cerebellum	3.01 RPM	50.63 RPM
SRP021940_embryo	2.71 RPM	40.79 RPM
SRP021940_placental_villous	1.40 RPM	27.18 RPM
SRP021940_synovial_membrane	2.09 RPM	25.78 RPM
SRP021940_testis	0.90 RPM	48.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1064 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1064 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006438	1 retrocopy	retro_amel_1830,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
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,