RetrogeneDB ID: retro_amel_866

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192695.1:53824..54220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000005734
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZMAT5
• Ensembl ID: ENSAMEG00000008059
• Aliases: None
• Description: zinc finger, matrin-type 5 [Source:HGNC Symbol;Acc:28046]

Sequence

>retro_amel_866
CTGGGGAAGCATCACTCCTGTGACGACTGCAGCTGCTCCTTCCAGGACAACCTCCACAACGGCAGAAGCTCCTGAATGGG
CTGCGGCACCTCAAGGCCAACAAGGTCTGCTATGATGTATTCCAAGATGCAGCTGCCATCTTGCTAGATGAACAGGAAGA
GTGGTCCTGCAGGAAGTTTCTACCGACAGGCCAGTGTGCCTTTGGCTGCAACTGCAGATTTTCCCACATGTCAGAGACAG
ACCTGCAGGAGCTCAGTATCCAGGTGGAGGAGGAGAGGTGGGCCAGGGAGTGGCCACCAGAGGTCACTGAGCTCCCTGAG
GGCCATCTGGAAGACTGGTTGGAAAAGAGAGCCAAGCAGCTGAGCTCAGCCCCAAGCAAGCAGGGCTGAACCTGGG

Alignment

ORF - retro_amel_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKHYFCDYCNRSFQDNLHN-RKKHLNGLQHLKAKKVWYDMFRDAAAILLDEQNKRPCRKFLLTGQCDFG
          .GKH..CD.C..SFQDNLHN.R.K.LNGL.HLKA.KV.YD.F.DAAAILLDEQ....CRKFL.TGQC.FG
Retrocopy LGKHHSCDDCSCSFQDNLHN<RQKLLNGLRHLKANKVCYDVFQDAAAILLDEQEEWSCRKFLPTGQCAFG

Parental  SNCRFSHMSERDLQELSIQVEEERRAREWPLDVVELPEGHLEDWLEKRAKRLSLAPS-SRADSG
          .NCRFSHMSE.DLQELSIQVEEER.AREWP..V.ELPEGHLEDWLEKRAK.LS.APS.SRA..G
Retrocopy CNCRFSHMSETDLQELSIQVEEERWAREWPPEVTELPEGHLEDWLEKRAKQLSSAPS>SRAEPG

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_866 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_866 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008059	1 retrocopy	retro_amel_866 ,
Canis familiaris	ENSCAFG00000012343	2 retrocopies	retro_cfam_1130, retro_cfam_1424,
Cavia porcellus	ENSCPOG00000020994	1 retrocopy	retro_cpor_1043,
Echinops telfairi	ENSETEG00000003789	2 retrocopies	retro_etel_2098, retro_etel_421,
Felis catus	ENSFCAG00000004251	1 retrocopy	retro_fcat_824,
Myotis lucifugus	ENSMLUG00000017398	1 retrocopy	retro_mluc_568,
Mustela putorius furo	ENSMPUG00000013253	1 retrocopy	retro_mputfur_875,