RetrogeneDB ID: retro_amel_1188

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193021.1:385842..386418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000012307
• Aliases: None
• Description: None

Sequence

>retro_amel_1188
GCACGCACAGGTAAAGCCCACCCCAGACTTGCAGCCACCTCTGTAGTGGACGTAAACTTCGAGGAGGTGAAGCTTTCTGA
CCACAGAGCCAAATACTTCGGTTCTGTTTTCCTACCCGCTGGACCTCGCCTTTTGTCTGCCCCATGGACATCGCTTTCAG
AGAATATGCTGGGGACTCTCACAAGCTAGGCTGGTAGCTGCTGGGGTCTCTGTCTACTCTCAGTTCGCCCACCTGGCTTG
GATCAATACTCCCGAGAAGGAGGGAGGCTGGGACCCTCTGAACACGCCCCTGCTGACTGGTGTAACCAGAAGCTTGTCCC
GAGATTATGGAGTGCTGAAGGAAGATGAGGGCACTGCCTACAGGGGCCTCTTCATAATCCATGGCAAGGGTGCCCTTCAC
GAGCTCACTCTCAATGATTTGCCAGTGGGTGCTCCATGCACACAGCTCTGCAGCTGGCCCGGGACTTCCAGTACACAGAC
GCGCATGGGGAAATCCGTCCCACTGGATGCAAGCCAGGCAGCGACACAATCAAGCCCACTGTGCACGACTGCAAGGAATA
CTTCTCCAAACACAAC

Alignment

ORF - retro_amel_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.47 %
• Parental protein coverage: 96.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AHIGEPAPPFQATAVVDGAFKEVKLCDYKGKYL-VLFFYPLDFTF-VCPTEIIAFSERAEDFRKLGCEVL
          A..G...P...AT.VVD..F.EVKL.D...KY..VLF.YPLD..F.VCP..I.AF.E.A.D..KLG...L
Retrocopy ARTGKAHPRLAATSVVDVNFEEVKLSDHRAKYF>VLFSYPLDLAF>VCPMDI-AFREYAGDSHKLGW*LL

Parental  G-VSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTRNLSEDYGVLKKDEGIAYRGLFIIDGKGVLRQIT
          G.VSV.SQF.HLAWINTP.KEGG..PLN.PLL..VTR.LS.DYGVLK.DEG.AYRGLFII.GKG.L...T
Retrocopy G<VSVYSQFAHLAWINTPEKEGGWDPLNTPLLTGVTRSLSRDYGVLKEDEGTAYRGLFIIHGKGALHELT

Parental  VNDLPVGR-SVDEVLRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
          .NDLPVG..S....L.L...FQYTD.HGE..P.G.KPGSDTIKP.V.D.KEYFSKHN
Retrocopy LNDLPVGA<SMHTALQLARDFQYTDAHGEIRPTGCKPGSDTIKPTVHDCKEYFSKHN

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_1188 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1188 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 22 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188 , retro_amel_1710, retro_amel_55,
Ailuropoda melanoleuca	ENSAMEG00000013632	2 retrocopies	retro_amel_1116, retro_amel_539,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,