RetrogeneDB ID: retro_amel_645

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192543.1:740446..741305(+)
• Located in intron of: ENSAMEG00000013906

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000018116
• Aliases: None
• Description: Autophagy-related protein 3 [Source:UniProtKB/TrEMBL;Acc:G1MIG3]

Sequence

>retro_amel_645
AAGGAAACAGGTGTTATCACCCCCAGAAGAGTTTGTGGCAGCTGGAGATCACTTAAGTCTGCCACTGTCCAACCTGGCAA
TGCACTACAGGGGAAGAATTGAAAGTGAAGGCATACCTACCAACAGGCAAACAATTTTTGGTCACCAAAAATGTGCCATG
CTACAAGCGGTGCAAACAGATGGAATATTCAGATGAATCGGAAGCTATCAGTGAAGAAGATGATGGTGATGGGGGATGGG
TAGATACTTATCATAACACAGGAATTGCAGGAATAACTGAAGCAGTAAAGGAGATTACGTTGGAAAGCAAGGACAGTGTA
AAACTTCAAGATTGCTCAGCAATATGTGAGGAGGAGGAGGAAGAAGATGAAGGAGAAGTTGCAGATATGGAAGAATATGA
AGAAAGAGGATTGTTGGAAACAGATGAGGCTACCCTAGACACAAGGAAAATAGTAGAAGCTTGTAAAGCTAAAACTGATG
CTGAAGGTGAAGATGCTATTTTGCAAACAAGAACTTATGACCTTTATAGCACTTATGATACATATTACCAGAAACCATGA
CTATGGTTGTTCAGCTATGATGAGCAAAGGCAACCTTTAACAGTTGAACACATGTATGAAGACATCAGCGAAGATCATGT
GAAGAAAAGAGTAAACACTGAAAATCACCCTCATCTCCCACTGCCTCCTATGCGTTCAGTTCACCCACGCAGGCATACTG
AGGTGATGAAGAAAATCATTGAGACTGTTGCAGAAGGAGGGGGAGAACTGGTGTTCATATGTATCTTCTAATTTTCTTGA
AGTTTGTACAAGCTGTCATTCCAACAATAGAAGATGACTATACAAGACATTTTACAATA

Alignment

ORF - retro_amel_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.97 %
• Parental protein coverage: 91.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KETGVITP-EEFVAAGDHL-VHHCPTWQWATGEEFKVKAYLPTGKQFLVTKNVPCYKRCKQMEYSDELEA
          KETGVITP.EEFVAAGDHL.V.HCPTWQ..TGEE.KVKAYLPTGKQFLVTKNVPCYKRCKQMEYSDE.EA
Retrocopy KETGVITP>EEFVAAGDHL>VCHCPTWQCTTGEELKVKAYLPTGKQFLVTKNVPCYKRCKQMEYSDESEA

Parental  IIEEDDGDGGWVDTYHNTGIAGITEAVKEITLESKDSIKLQDCLAVCEEEEEEDEGEAADMEEYEESGLL
          I.EEDDGDGGWVDTYHNTGIAGITEAVKEITLESKDS.KLQDC.A.CEEEEEEDEGE.ADMEEYEE.GLL
Retrocopy ISEEDDGDGGWVDTYHNTGIAGITEAVKEITLESKDSVKLQDCSAICEEEEEEDEGEVADMEEYEERGLL

Parental  ETDEATLDTRKIVEACKAKTDAEGEDAILQTRTYDLYITYDKYYQTPRLWLFGYDEQRQPLTVEHMYEDI
          ETDEATLDTRKIVEACKAKTDAEGEDAILQTRTYDLY.TYD.YYQ.P.LWLF.YDEQRQPLTVEHMYEDI
Retrocopy ETDEATLDTRKIVEACKAKTDAEGEDAILQTRTYDLYSTYDTYYQKP*LWLFSYDEQRQPLTVEHMYEDI

Parental  SQDHVKKTVTIENHPHLPPPPMCSVHPCRHAEVMKKIIETVAEGGGEL-GVHMYLLIFLKFVQAVIPTIE
          S.DHVKK.V..ENHPHLP.PPM.SVHP.RH.EVMKKIIETVAEGGGEL.GVHMYLLIFLKFVQAVIPTIE
Retrocopy SEDHVKKRVNTENHPHLPLPPMRSVHPRRHTEVMKKIIETVAEGGGEL<GVHMYLLIFLKFVQAVIPTIE

Parental  YDYTRHFTM
          .DYTRHFT.
Retrocopy DDYTRHFTI

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_645 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_645 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645 ,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268, retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,