RetrogeneDB ID: retro_amel_1830

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194647.1:31341..32889(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000003328
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZXDC
• Ensembl ID: ENSAMEG00000006438
• Aliases: None
• Description: ZXD family zinc finger C [Source:HGNC Symbol;Acc:28160]

Sequence

>retro_amel_1830
CCCCGCAGGCCGCTGGGCCCAGGCGTGGTGCTGTACCTGTGTCCCGAGGCGCAGTGCGGACAAACCTTCGCCAAGAAGCA
CCAGCTGAAGGTGCACCTGCTGACTCACAGCAGCAGCCAGGGCCAACGGCCCTTCAAGTGCCCCCTGGGCGGCTGTGGCT
GGACTTTCACCACCTCCTACAAGCTCAAGAGGCACCTGCAGTCTCACGACAAGCTGCGGCCCTTTGGCTGCCCTGCGGAG
GGCTGTGGCAAGAGCTTCACCACGGTGTATAACCTCAAGGCGCACATGAAGGGCCATGAGCAGGAGAATTCGTTCAAATG
CGAGGTGTGCGAGGAGAGCTTCCCCACTCAGGCCAAACTCAGCGCCCACCAGCGCAGCCATTTCGAGCCCGAGAGGCCGT
ACCAGTGCGCGTTTTCCGGCTGCAAGAAGACGTTTATCACAGTGAGTGCCCTGTTTTCCCACAACCGTGCCCATTTCAGG
GAACAGGAACTCTTTTCCTGCTCTTTTCCTGGCTGCAGCAAACAGTACGACAAGGCTTGTCGCCTGAAAATTCACCTGCG
GAGCCACACCGGTGAGAGACCTTTCCTTTGTGACTTTGACGGCTGTGGCTGGAACTTCACCAGCATGTCCAAACTCTTAA
GGCACAAAAGGAAGCACGAGGATGACCGGAGGTTCATGTGCCCCGTGGAAGGCTGTGGGAAATCTTTCACAAGGGCTGAA
CATCTGAAAGGCCACAGCATAACCCACCTGGGCACAAAGCCTTTTGTGTGCCCTGTGGAAGGCTGCTGTGCCAGGTTCTC
TGCTCGCAGTAGTCTCTACATTCACTCCAAGAAACACTTGCAGGACGTGGACACTTGGAAAAGCCGTTGCCCAGTCTCTA
CTTGTAATAAACTCTTCACATCCAAGCACAGCATGAAGACCCACATGGCCAAAAGGCACAACCTCGGCCAGGATCTTTTA
GCTCAGCTAGAAGCTGCAAATTCTCTTACACCCAGCAGTGAACTTACCAGCCAGGGACAGAGTGATCTCAGTGATGCAGA
GCTAGTGTCTCTCTTCTCTGATGTGCCTGGCAGTAGTTCTGCTACAGTGCTGGACACAGCATTGGTGAACTCTGGAATCT
TGACTATTGATGTGGCTTCTGTGAGTTCAACTCTGGCAGGGAGCCTCCCTGCTAATAATAATAATTCCTTAGGGCAGGCT
GTGGACCCTCGGGCCTTGATGGCCACCAGTGACCTTCCTCAAAGTCTGGATACCTCTCTTTTTTTTGGAACGACAGCCTC
TGGTTTTCAGCAGAGTCCCTTAGATATGGATGATGTCCCAAGTCTGACTGTGGGGCCGTTGGCATCTCTGGGCTCTTCGG
CTATGAAAAACTCGAGTCAAGAGCCCCAAGCTCTGACCCCTAGCAGTAAGCTAACAGTGGACACAGATGCCCTGACTCCT
TCAAGCACCCTTTGTGAAAACAGTGTCTCAGAACTACTGCCGCCAACCAAAGCAGAATGGAATGTACATCCTGACTCCGA
CTTCTTTGGACAGGAGGAAGAAACCCAG

Alignment

ORF - retro_amel_1830 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 73.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PARQAXPG---YRCPEPQCALSFAKKHQLKVHLLTHSSSQGRRPFKCPLDGCGWAFTTSYKLKRHLQSHD
          P.R...PG...Y.CPE.QC...FAKKHQLKVHLLTHSSSQG.RPFKCPL.GCGW.FTTSYKLKRHLQSHD
Retrocopy PRRPLGPGVVLYLCPEAQCGQTFAKKHQLKVHLLTHSSSQGQRPFKCPLGGCGWTFTTSYKLKRHLQSHD

Parental  KLRPFGCPVGGCGKKFTTVYNLKAHMKGHEQENLFKCEVCSERFPTHAKLSSHQRSHFEPERPYKCDFPG
          KLRPFGCP..GCGK.FTTVYNLKAHMKGHEQEN.FKCEVC.E.FPT.AKLS.HQRSHFEPERPY.C.F.G
Retrocopy KLRPFGCPAEGCGKSFTTVYNLKAHMKGHEQENSFKCEVCEESFPTQAKLSAHQRSHFEPERPYQCAFSG

Parental  CEKTFITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFICDSDSCGWTFTSMS
          C.KTFITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPF.CD.D.CGW.FTSMS
Retrocopy CKKTFITVSALFSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFLCDFDGCGWNFTSMS

Parental  KLLRHKRKHDDDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFECPVEGCCARFSARSSLYIHSKKHL
          KLLRHKRKH.DDRRF.CPVEGCGKSFTRAEHLKGHSITHLGTKPF.CPVEGCCARFSARSSLYIHSKKHL
Retrocopy KLLRHKRKHEDDRRFMCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIHSKKHL

Parental  QDVGAPKSRCPVSSCNRLFTSKHSMKAHVVRQHSRRPDLFPQLGAPSSLTHSSELGSPGQSELNNIDLAA
          QDV...KSRCPVS.CN.LFTSKHSMK.H....H....DL..QL.A..SLT.SSEL.S.GQS.L....L..
Retrocopy QDVDTWKSRCPVSTCNKLFTSKHSMKTHMAKRHNLGQDLLAQLEAANSLTPSSELTSQGQSDLSDAELVS

Parental  LFSDAPGDGGSVAGASDEAL-NSGILTIDVTSVSASLGGNLPA-NNSSLG-PMDPLVLVAHSDISPSLDS
          LFSD.P..G.S.A...D.AL.NSGILTIDV.SVS..L.G.LPA.NN.SLG...DP..L.A.SD...SLD.
Retrocopy LFSDVP--GSSSATVLDTALVNSGILTIDVASVSSTLAGSLPANNNNSLGQAVDPRALMATSDLPQSLDT

Parental  PLVLGTAATVLQQSSFSVDDVPTVSAGALGCLVALPVKNLSPDPQALTSGGHLADTTTTLTSPSPAPGNT
          ....GT.A...QQS....DDVP....G.L..L.....KN.S..PQALT....L...T..LT.PS......
Retrocopy SXXXGTTASGFQQSPLDMDDVPSLTVGPLASLGSSAMKNSSQEPQALTPSSKLTVDTDALT-PSSTLCEN

Parental  GGPELLAPIKVEPDSPPGPNAARQQERSR
          ...ELL.P.K.E....P......Q.E...
Retrocopy SVSELLPPTKAEWNVHPDSDFFGQEEETQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1830 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1830 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,