RetrogeneDB ID: retro_amel_1035

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192849.1:1197667..1198118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSAMEG00000000829
• Aliases: None
• Description: None

Sequence

>retro_amel_1035
GTGTTTGAAAAAAGTGGGATAATGGATACAGTACAATCTGGAAAAGGTTCTAGGATTAACAAAATGGCTTATCCACTGGG
ACTGGCCACTGTAGGAGCAACTGTTTGCTACCCAGTTCAGTCAGTAATAATTGCAAAGGTAACTGGGAAAAAGGCATATA
CTACAAGCCAGCAAATTTAGGAAGCAGTTAAATCACTGCAGACAAAAATCAGCAAGAGTCATTTCCTAAATCTAAAGAAA
AAGCTAAGCTAGGAAATTCTGCTGAAATAGAAATACCTGTAAAAACAACGGACAGCCTGAAATACTCAGTACCCTTGCCA
ATAGAACTCAGCTCTGAAACAAAGACAAAATCAGAATCCCCCTCGGGTGCTACCTAGTTTATGCCTGACCCCAAGCCCAT
GGATCACAGCCAGTCCCATCCAGAATATGTGGAGTGTACAGCACTAGAAGC

Alignment

ORF - retro_amel_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 57.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VITVSGLAGLVSARKGSRFKKIAYPLGLATLGATVCYPVQSVIIAKVTGKKAYTTSQQIYEAVKSLWTKM
          V...SG....V...KGSR..K.AYPLGLAT.GATVCYPVQSVIIAKVTGKKAYTTSQQI.EAVKSL.TK.
Retrocopy VFEKSGIMDTVQSGKGSRINKMAYPLGLATVGATVCYPVQSVIIAKVTGKKAYTTSQQI*EAVKSLQTKI

Parental  NKKESFPKPKEK-SKLGNSAEIEIPAKTTDSLKHSVPLPTELSSETKTKSESTSGATQFMPDPKLMDYGQ
          .K...F...K.K..KLGNSAEIEIP.KTTDSLK.SVPLP.ELSSETKTKSES.SGAT.FMPDPK.MD..Q
Retrocopy SKSH-FLNLKKK<AKLGNSAEIEIPVKTTDSLKYSVPLPIELSSETKTKSESPSGAT*FMPDPKPMDHSQ

Parental  SHPEDID-MYSTRS
          SHPE.....YSTRS
Retrocopy SHPEYVE<VYSTRS

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_1035 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1035 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 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035 ,
Ailuropoda melanoleuca	ENSAMEG00000012749	1 retrocopy	retro_amel_1282,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,