RetrogeneDB ID: retro_amel_1480

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193470.1:550553..550952(+)
• Located in intron of: ENSAMEG00000008480

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSAMEG00000003968
• Aliases: None
• Description: 6-pyruvoyltetrahydropterin synthase [Source:HGNC Symbol;Acc:9689]

Sequence

>retro_amel_1480
GCACATCTGTCCCACCTCATGTCCTTCAGAAGACCCACCGGCTCCACAGCAAATCTCTGAGTAATGAAGAAAACTTGAAA
CTGTTTGGGACCTGCAACAGTCCAAATGGCTGTGGGCACAATTATACAGTTGTGGTGACAGTACATGGAGAGACTGATCC
TGTTACAAGCAACGGTTATAAATCTGACCAACCTCAAGGAGTATATGGAGGAAATTATGAAGGCCTTTGATCGTAAGAAT
CTAGATCTGAATGGGCCATACTTTGCAGTTGTTGTACGCATGACAGAAAATGTAGCCGTATGTATCTGGGGAAACCTCCA
GAAATTTTTTCCTCTGGGTGTTCTTTATGAAGGAAAAGTATATGAAGCTGACAATAATATTGTCGTCTATAAAGGAGAA

Alignment

ORF - retro_amel_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 91.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARVSRLVSF-SATHRLHSKSLSNEENLKLFGKCNNPNGHGHNYKVVVTVHGEIDPVTG-MVMNLTDLKEY
          A..S.L.SF...THRLHSKSLSNEENLKLFG.CN.PNG.GHNY.VVVTVHGE.DPVT...V.NLT.LKEY
Retrocopy AHLSHLMSF<QKTHRLHSKSLSNEENLKLFGTCNSPNGCGHNYTVVVTVHGETDPVTS>TVINLTNLKEY

Parental  MEEAIMKPLDHKNLDLDVPYFADVVSTTENVAVYIWENLQKFLPLGVLYKVKVYETDNNIVVYKGE
          MEE.IMK..D.KNLDL..PYFA.VV..TENVAV.IW.NLQKF.PLGVLY..KVYE.DNNIVVYKGE
Retrocopy MEE-IMKAFDRKNLDLNGPYFAVVVRMTENVAVCIWGNLQKFFPLGVLYEGKVYEADNNIVVYKGE

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_1480 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1480 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003968	3 retrocopies	retro_amel_1001, retro_amel_1480 , retro_amel_691,
Bos taurus	ENSBTAG00000003770	3 retrocopies	retro_btau_1182, retro_btau_1762, retro_btau_682,
Canis familiaris	ENSCAFG00000013915	2 retrocopies	retro_cfam_1386, retro_cfam_1859,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Felis catus	ENSFCAG00000024702	3 retrocopies	retro_fcat_1546, retro_fcat_212, retro_fcat_564,
Myotis lucifugus	ENSMLUG00000023388	1 retrocopy	retro_mluc_946,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Sorex araneus	ENSSARG00000001975	2 retrocopies	retro_sara_163, retro_sara_72,
Sus scrofa	ENSSSCG00000015040	1 retrocopy	retro_sscr_284,
Tursiops truncatus	ENSTTRG00000010526	1 retrocopy	retro_ttru_1710,
Vicugna pacos	ENSVPAG00000000061	1 retrocopy	retro_vpac_363,