RetrogeneDB ID: retro_amel_1176

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193010.1:397274..397566(+)
• Located in intron of: ENSAMEG00000007701

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010854
• Aliases: None
• Description: None

Sequence

>retro_amel_1176
TGCTGCTACAGCTTCGAGAACAAGTACTTGAACCAGGATCGAGAGGAGCGGAAGCTGCTGCTGGACCCTAGCGCCCCCCC
TTACCAAAGCCCTCAGTGCAGCTGAGCCCAACTATCGCAGCCTGCATCACGGCTCGCACAGATGAGCGGGCTCTGCTCTC
CCCCGTCCCTGTTAAGATAGCCAGCAACATCCCCTTAGTGTCTGCTGCAGACTCCCAGGGCATGGACAGCACGAATACAC
GGACCCGGCAAGGCAGCACAGCACCCGCTTGGCTGTGCGGCACAACAGGCTG

Alignment

ORF - retro_amel_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69. %
• Parental protein coverage: 60.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CCYSSENEDSDQDREERKLLLDPSSPP-TKALNGAEPNYHSLP-PTRTDEQALLSSILAKTASNIIDVSA
          CCYS.EN....QDREERKLLLDPS.PP.TKAL..AEPNY.SL....RTDE.ALLS....K.ASNI..VSA
Retrocopy CCYSFENKYLNQDREERKLLLDPSAPP>TKALSAAEPNYRSLH>TARTDERALLSPVPVKIASNIPLVSA

Parental  ADSQGME-QHEYMDRARQYSTRLAVLSSSL
          ADSQGM..QHEY.D.ARQ.STRLAV....L
Retrocopy ADSQGMD<QHEYTDPARQHSTRLAVRHNRL

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_1176 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1176 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176 , retro_amel_436,
Canis familiaris	ENSCAFG00000005788	1 retrocopy	retro_cfam_1962,
Echinops telfairi	ENSETEG00000010979	1 retrocopy	retro_etel_1005,
Felis catus	ENSFCAG00000005320	2 retrocopies	retro_fcat_142, retro_fcat_496,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Myotis lucifugus	ENSMLUG00000014117	1 retrocopy	retro_mluc_2372,
Mustela putorius furo	ENSMPUG00000010289	3 retrocopies	retro_mputfur_1178, retro_mputfur_270, retro_mputfur_455,
Mus musculus	ENSMUSG00000030842	2 retrocopies	retro_mmus_1805, retro_mmus_2538,
Rattus norvegicus	ENSRNOG00000020016	1 retrocopy	retro_rnor_2788,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,