RetrogeneDB ID: retro_amel_1899

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195414.1:27322..27716(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSAMEG00000008426
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_amel_1899
GAGACATCTGCTTCTGGAGCTGTGGCCATCACATTCCCAGGTTCAGCAGGCCACTGAGTGCGCCTGGTACCAGAAGCATG
TGCCTCCAGTCCCTGAGTCCTGACTGCCCTCGTTCCACTGCCAACCTTCTCAGCCAGTCATGCTGGATCATCTGAGATCA
CTCCCTACACAAATGGATTACAAGGGCCAGAATCTAGCTGAACAGATGGTTCAGGGAATAATTCTTTTTCCTGCAATAGT
TGGATTTATCTATGGGTATGTGGCTGAACAGTTCAAGTGGACTGTCTATATAGTTATGATTGGATTTGCTTTGTCATGCT
TGTTGACACTTCCTCCATGGCCCAGTTATCACTGACATCCCCTCAAGTGGTTACCTGTTCAAGCCTCAGGCTCA

Alignment

ORF - retro_amel_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.61 %
• Parental protein coverage: 81.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETSASGATAIAF-PGTAGPSS-CPWYQTPAPRVPKSRLPSAGCQPSQPVMLQHLSSLPTQMDYKGQKLAE
          ETSASGA.AI.F.P....P.S.C.WYQ...P.VP.S.LPS..CQPSQPVML.HL.SLPTQMDYKGQ.LAE
Retrocopy ETSASGAVAITF<PRFSRPLS<CAWYQKHVPPVPES*LPSFHCQPSQPVMLDHLRSLPTQMDYKGQNLAE

Parental  QMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYRRHPLKWLPVQDSGS
          QM.QGIILF.AIVGFIYGYVAEQF.WTVYIVM.GFA.SCLLTLPPWP.Y..HPLKWLPVQ.SGS
Retrocopy QMVQGIILFPAIVGFIYGYVAEQFKWTVYIVMIGFALSCLLTLPPWPSYH*HPLKWLPVQASGS

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_1899 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1899 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899 ,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,