RetrogeneDB ID: retro_amel_519

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192484.1:2232063..2232414(+)
• Located in intron of: ENSAMEG00000008948

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSAMEG00000012653
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_amel_519
ATGTCTTCTGAAGAAGGGAAGATTTTCGTGGGAGGGCTCAACTTCAACCCCAATAAGCAGGCTCTGGAAGACCACTTGAG
CAGCTCTGGCCCTATTTCTGAGGTGGCTGTTGTCAAGGACTTGTGAGACTCAGCAATCCTGGGGTTTTAGTTTCATCACC
TTCACCAAACCAGAGTGTGTCTCAGGTGCCAAGCGAGCCATAAATGGAGAGTCTCTGGCTGGTCAGCAGATCCACACGGA
TCACTCTGGCAAGTCAGCCAGGGGAACGGGAGGGGGTGCCTTTGGGGCCCCGGGGCAAGGTTGCAGCCACCTGGTGGTGG
GGACCAGGGCTATGGGGGTGGCAGGTATGAT

Alignment

ORF - retro_amel_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.67 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDR-ETQRSRGFGFITFTNPEHASDAMRAMNG
          MSSEEGK.FVGGLNFN...QALEDH.SS.GPISEV.VVKD..ETQ.S.GF.FITFT.PE..S.A.RA.NG
Retrocopy MSSEEGKIFVGGLNFNPNKQALEDHLSSSGPISEVAVVKDL>ETQQSWGFSFITFTKPECVSGAKRAING

Parental  ESLDGRQIRVDHAGKSARGTRGGAYGAHGRGRSY-SRGGGDQGYGSGRYD
          ESL.G.QI..DH.GKSARGT.GGA.GA.G.G.S....GG.DQGYG.GRYD
Retrocopy ESLAGQQIHTDHSGKSARGTGGGAFGAPGQGCSH<PGGG-DQGYGGGRYD

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_519 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_519 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 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519 ,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,